Digital Tools & Resources: Difference between revisions
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== | ==How to use this page== | ||
'''Please help us by adding new digital resources useful to the community here. Keep this page organized by following the <br /> | |||
'''format and alphabetical organization already in place.''' | |||
All of the links below are organized first by whether they are general reference or a more specified research tool. <br /> | |||
The sub-categories are organized alphabetically by research topic. Note that many of the tools listed may fit into <br /> | |||
multiple categories, but are only listed once. Tools of this type may be tagged with other relevant categories by <br /> | |||
adding a link to another section of the page after the description. Use the <sub>[http://en.wikipedia.org/wiki/Help:Link#Section_linking_.28anchors.29 *link]</sub> format of the following [[Digital Tools & Resources#DNA_2|DNA]] example: | |||
=== | <code> | ||
[http://qiime.org/ QIIME] (Quantitative Insights Into Microbial Ecology) <sup><sup>software</sup></sup> <br /> | |||
Powerful suite of open source bioinformatics tools for performing microbiome analysis from raw sequences. <sub>[[Web resources#RNA_2|*RNA]]</sub> | |||
</code> | |||
This allows for quick navigation around the page and the use of the * in '''Ctrl + F''' searches to differentiate between <br /> | |||
sections and page body content. | |||
Please help keep this page up to date by fixing old or broken links and by deleting listings that no longer work. If <br /> | |||
you think that an item has been placed in the wrong category, feel free to move it. Please be cautious when downloading <br /> | |||
software, and make sure to help the community by removing links with harmful content. Content with questionable scientific <br /> | |||
value should also be removed. | |||
All information resources are assumed to be online, but research tools should be tagged with <sup><sup>web</sup></sup> for online resources, <sup><sup>software</sup></sup> <br /> | |||
for downloadable items, and <sup><sup>app</sup></sup> for items used on phones and tablets. Please tag any additional categories in this <br /> | |||
way if needed. Additional suggestions for format changes may be executed directly or discussed on the talk page. | |||
<!-- These whitespaces are in place to separate the TOC from the next section. --> | |||
<!-- Move or edit them if necessary to preserve formatting --> | |||
<!-- and may your science be successful today --> | |||
==<span id="Information Resources"></span>Information resources== | |||
'''References, texts, and information resources.''' | |||
===Databases=== | |||
''Search engines and data repositories. There are thousands available (see [[MetaBase]]). The few items listed here are some of the broadest and most powerful'' | |||
====<span id="General Search/Reference"></span>General Search/Reference==== | |||
* [[BioNumbers]] | |||
** The database of useful biological numbers. [http://bionumbers.hms.harvard.edu/ (link to database)] | |||
* [http://www.cdc.gov/DiseasesConditions/az/A.html CDC Disease Conditions] | |||
** Filtered index of diseases from the CDC database | |||
* [http://www.ebi.ac.uk/ EMBL-EBI] | |||
** Hugely extensive collection of resources, databases, and tools related to diverse aspects of bioinformatics and molecular biology, often containing everything one might need | |||
* [http://www.ncbi.nlm.nih.gov/sites/gquery Entrez (NCBI)] | |||
** Search all NCBI databases | |||
* [[MetaBase]] | |||
** The database of biological databases - [http://BioDatabase.Org External link] | |||
* [http://tolweb.org/tree/ Tree of Life] | |||
** Collaborative encyclopedia of biodiversity | |||
*[http://www.wolframalpha.com/ Wolfram Alpha] | |||
** Computational server for finding/calculating summary data about a wide range of topics, plus useful widgets like [http://www.wolframalpha.com/widgets/view.jsp?id=25abc22f639d44dd55ba9c02ff8958f0 reagent tables] and [http://www.wolframalpha.com/widgets/view.jsp?id=3088112560cd18b00cbf34a95b024d06 gene lookup] | |||
====<span id="Genome and Metabolism"></span>Genome and Metabolism==== | |||
*[http://biocyc.org/ BioCyc] | *[http://biocyc.org/ BioCyc] | ||
**Collection of thousands of pathway/genome databases, plus software tools for understanding their data | **Collection of thousands of pathway/genome databases for many organisms, plus software tools for understanding their data | ||
*[http:// | *[http://genolist.pasteur.fr/Colibri/ Colibri] by Institut Pasteur | ||
** | **''E. coli'' genome browser; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the ''E. coli'' genome. | ||
*[http://ecogene.org/index.php EcoGene] | *[http://ecogene.org/index.php EcoGene] | ||
**Database of all E. coli genes and sequences | **Database of all E. coli genes and sequences (Entrez data is pulled from here) | ||
*[http://ecocyc.org | *[http://ecocyc.org EcoCyc] | ||
** Comprehensive biochemical pathway and gene function site for ''E. coli'' | ** Comprehensive biochemical pathway and gene function site for ''E. coli'' | ||
=== | *[http://genome.ucsc.edu/ENCODE/ ENCODE] | ||
*[[ | **Parts list for functional elements in the human genome | ||
** | |||
*[http://useast.ensembl.org/index.html Ensembl] | |||
**Eukaryotic genome browser | |||
*[http://ensemblgenomes.org/ Ensembl Genome] | |||
**Sister to Ensembl, not limited to Eukaryotes | |||
*[http://public-registry.jbei.org Inventory of Composable Elements (ICE)] - The public instance of the JBEI Registry | |||
** A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities | |||
** A site where you can explore the various features of the JBEI Registry software, and even get some work done! | |||
** Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template. | |||
** Follow a link to the underlying open-source software source code. | |||
*[http://www.genome.jp/kegg/ KEGG] | |||
**Genomic database geared towards high-level functions of the biological system | |||
*[http://mgc.nci.nih.gov/ Mammalian Gene Collection] | |||
**Access to sequence-validated, full-length, protein-coding, mammalian cDNA clones | |||
*[http://metacyc.org/ MetaCyc] | |||
**Multi-organismal member of BioCyc collection; catalogs entire universe of metabolism | |||
*[http://www.yeastgenome.org/ SGD] | |||
**Saccharomyces genome database (yeast genome) | |||
*[http://genome.ucsc.edu/index.html UCSC Genome Bioinformatics] | |||
**Sequence reference for a large number of genomes | |||
====<span id="Protein"></span>Protein==== | |||
*[http://www.antibodyresource.com/ Antibody Resource] | |||
**Enter a protein to search for antibodies and ELISA kits | |||
*[http://www.brenda-enzymes.org/ BRENDA] | |||
**Comprehensive enzyme information system | |||
*[http://www. | *[http://consurf.tau.ac.il/ ConSurf] | ||
**Server for the identification of functional regions in proteins | |||
*[http://genome3d.eu/ Genome3D] | |||
**Consensus structural annotations and 3D models for sequences of model organisms (built upon numerous other useful related resources) | |||
*[http://www.hamptonresearch.com/support/ Technical suppport on protein crystallization] by Hampton Research | |||
**Focused on protein crystallization but contains a lot of generally useful information about various reagents with respect to proteins. | |||
*[http://www.uniprot.org/ UniProt] | |||
**Extensive database of protein sequence and functional information | |||
====<span id="RNA"></span>RNA==== | |||
*[http://www.ambion.com/techlib/append/na_mw_tables.html Appendix] by Ambion, Inc. | |||
**Website with many useful nucleic acid parameters. | |||
*[http://greengenes.lbl.gov/cgi-bin/nph-index.cgi GreenGenes] | |||
** 16S rRNA database and workbench (most recently updated data can be downloaded [http://greengenes.secondgenome.com/downloads here]) | |||
*[http://rdp.cme.msu.edu/ Ribosomal Database Project] | |||
**Quality-controlled, aligned and annotated Bacterial and Archaeal 16S rRNA sequences, and Fungal 28S rRNA sequences, and a suite of analysis tools | |||
*[http://www.arb-silva.de/ SILVA] | |||
**Massive, searchable rRNA database (especially strong for microbes) | |||
====<span id="Vectors"></span>Vectors==== | |||
*[http://www.addgene.org/vectors Addgene's Vector DB] | |||
**[http://www.addgene.org Addgene] is a a non-profit plasmid repository where scientists can archive and share their plasmids. Addgene assists with data submission and all tech transfer issues. Plasmids can be requested from Addgene for a fee to cover expenses. | |||
** AddGene Vectors can be directly imported into [http://www.genomecompiler.com/?utm_source=refferal_website&utm_medium=referral&utm_term=digital_tools_and_resources&utm_content=website&utm_campaign=openwetware Genome Compiler] software platform, in which you can easily edit and visualize it. | |||
===<span id="Lab Techniques"></span>Lab Techniques=== | |||
*[http://barricklab.org/twiki/bin/view/Lab/ProtocolList Barrick Lab] of UT Austin | |||
**Tons of helpful resources like protocols, guides, links, and tools for lab work | |||
*[http://www.benchfly.com/video-protocols BenchFly] | |||
**Search, view, upload, create, and host scientific protocol videos | |||
*[http://www.wiley.com/WileyCDA/WileyTitle/productCd-047150338X.html Current Protocols in Molecular Biology] | |||
**Handbook of protocols. (Links to Wiley Online Library) | **Handbook of protocols. (Links to Wiley Online Library) | ||
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*[[Molecular Cloning]] by Sambrook and Russell | *[[Molecular Cloning]] by Sambrook and Russell | ||
**Handbook of protocols. Subscription only. [http://www.molecularcloning.com/ External link] | **Handbook of protocols. Subscription only. [http://www.molecularcloning.com/ External link] | ||
*[http://openwetware.org/wiki/Materials OWW Materials] | |||
**Useful information for making or obtaining reagents, enzymes, buffers, etc. | |||
*[http://www.nap.edu/openbook.php?record_id=4917&page=R9 On Being a Scientist] by National Academy of Science | |||
**NAS report on responsible conduct in research. | |||
*[http://openwetware.org/wiki/Protocols OWW Protocols] | |||
**Growing collection of laboratory protocols and techniques | |||
*[http://arep.med.harvard.edu/polony/polony_protocols Polony Protocols] by Church and Mitra Lab | *[http://arep.med.harvard.edu/polony/polony_protocols Polony Protocols] by Church and Mitra Lab | ||
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**A database of research protocols in a variety of life science fields. It has a popular discussion forum. | **A database of research protocols in a variety of life science fields. It has a popular discussion forum. | ||
*[http:// | *[http://www.protocols.io/welcome Protocols.io] <sup><sup>app</sup></sup> <sup><sup>web</sup></sup> | ||
** VADLO is | **Huge, open access life science protocol repository for discovery and sharing of scientific methods | ||
*[http://vadlo.com/ VADLO Search Engine] | |||
** VADLO is a search engine for Life Sciences Protocols, Online Tools, Databases, Software, and Biomedical Powerpoint Lectures. It also has Daily research cartoons, called *[http://www.vadlo.com/Daily_Research_Cartoon.html "Life in Research" Cartoons]. | |||
===<span id="Microbial physiology"></span>Microbial physiology=== | |||
*[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi CyberCell Database (CCDB)] by Institute for Biomolecular Design | |||
**Several tables describing statistical data on ''E. coli'' compiled from several sources. | |||
*[http://www.ecosal.org/ecosal/index.jsp EcoSal] by ASM Press | |||
**An incomplete web version of the publication ''Escherichia coli and Salmonella: Cellular and Molecular Biology''. (Subscription required) | |||
*[http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/metabolic_pathways_poster.pdf Metabolic Pathways Poster PDF] by SigmaAldrich | |||
**Free digital version of the [http://www.sigmaaldrich.com/life-science/cell-biology/cell-biology-products.html?TablePage=14576275 paper Metabolic Pathways map]. Because it is a PDF, it is also searchable. | |||
*[http://microbewiki.kenyon.edu/index.php/MicrobeWiki MicrobeWiki] | |||
**Student edited resource on microbes and microbiology (curated pages reviewed by microbiologists) | |||
=== | ===<span id="Teaching"></span>Teaching=== | ||
*[http://www. | *[http://www.khanacademy.org/science/biology Khan Academy] (Biology) | ||
** | **Selection of science videos and short courses, including the popular ''[http://www.khanacademy.org/science/biology/crash-course-bio-ecology Crash Course]'' series | ||
*[http://phet.colorado.edu/ PhET] | |||
*[http:// | **Interactive simulations for science and math | ||
** | |||
*[http://sciencehack.com/videos/category/7 ScienceHack] | |||
*[http:// | **Search engine for science videos with a review system | ||
** | |||
== | ==<span id="Research Tools"></span>Research Tools== | ||
'''Tools | '''Tools and applications to aid in research tasks'''. | ||
===General=== | ===<span id="General"></span>General=== | ||
*[ | *[http://benchling.com/ Benchling] <sup><sup>web</sup></sup> | ||
** | **Online apps for cloning, molecular biology, and analysis | ||
*[ | *[http://www.dna20.com/index.php?pageID=216 Bioinformatics Toolbox] from DNA2.0 <sup><sup>web</sup></sup> | ||
**Contains many Javascript tools to do common tasks. | **Contains many Javascript tools to do common tasks. | ||
* | *[http://cgap.nci.nih.gov/cgap.html Cancer Genome Anatomy Project] <sup><sup>web</sup></sup> | ||
**Resources and tools related to the characterization of cancer gene expression profiles | |||
*[http:// | *[http://experiment.com/ Experiment] <sup><sup>web</sup></sup> | ||
** | **Crowdfunded scientific research | ||
*[http:// | *[http://genomecompiler.com/ Genome Compiler] <sup><sup>web</sup></sup> <sup><sup>software</sup></sup> | ||
** | **A powerful, free online & downloadable genetic engineering all-in-one platform for molecular & synthetic biologists | ||
*[ | *[http://primerdigital.com/fastpcr.html FastPCR] <sup><sup>software</sup></sup> | ||
** | **An integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching | ||
* | *[http://usegalaxy.org/ Galaxy] <sup><sup>web</sup></sup> | ||
** | **Easy-to-use Bioinformatics manipulation tools for UCSC data | ||
*[http://parts.igem.org/Main_Page iGEM Parts Registry] | *[http://parts.igem.org/Main_Page iGEM Parts Registry] <sup><sup>web</sup></sup> | ||
**Formerly curated by MIT, this is an open repository of BioBricks; the place for all your standard biological parts. | **Formerly curated by MIT, this is an open repository of BioBricks; the place for all your standard biological parts. | ||
*[[ | *[http://rusty.fhl.washington.edu/ingeneue/ Ingeneue] by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at the [http://www.celldynamics.org Center for Cell Dynamics] <sup><sup>software</sup></sup> | ||
** | **An open-source java program for modeling gene regulatory networks. Users can rapidly build networks by specifying their topology, initial conditions, connectivity, and known parameters. Ingeneue can then search/explore paramter space for desired behavior, simulate the effects of noise and mutation, and generate statistics/time graphs of the system. | ||
*[http://www. | *[http://www.phylogeny.fr/index.cgi MABL] <sup><sup>web</sup></sup> | ||
** | **Reconstruct and analyze phylogenetic relationships between molecular sequences | ||
* [http://parpar.jbei.org PaR-PaR Laboratory Automation Platform] | *[http://opencfu.sourceforge.net/ OpenCFU] <sup><sup>software</sup></sup> | ||
**Local cell colony counting software | |||
*[https://mcds.codeplex.com/ MCDS] <sup><sup>software</sup></sup> | |||
**All-in-one molecular cloning and genetic engineering design, simulation & management tool for complex synthetic biology and metabolic engineering project. | |||
*[http://parpar.jbei.org PaR-PaR Laboratory Automation Platform] <sup><sup>web</sup></sup> | |||
** PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour. | ** PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour. | ||
*[http://www.sciencegateway.org/ Science Gateway] | *[https://serotiny.bio Pinecone] by Serotiny <sup><sup>web</sup></sup> | ||
**High-level design, analysis and transmission of protein constructs. Pinecone matches users' designs with CRO's or DNA synthesizers to produce genetic starting material (dsDNA, plasmid or purified protein). Facilitates mutation and combinatorial protein sets that benefit from manufacturing economies of scale. | |||
*[http://www.pubchase.com/ PubChase] <sup><sup>software</sup></sup> <sup><sup>app</sup></sup> | |||
**Generates research article recommendations unique to each user. Site also has a special academic community. | |||
*[http://www.sciencegateway.org/ Science Gateway] <sup><sup>web</sup></sup> | |||
**Collection of science-related links, including links to journals, catalogs, and tools. See their [http://www.sciencegateway.org/about.htm about page]. | **Collection of science-related links, including links to journals, catalogs, and tools. See their [http://www.sciencegateway.org/about.htm about page]. | ||
===DNA=== | ===<span id="Calculators"></span>Calculators=== | ||
*[http:// | *[http://sosnick.uchicago.edu/gdmcl.html <nowiki>[GdmCl]</nowiki> and <nowiki>[Urea]</nowiki> from refractive index] by Sosnick lab <sup><sup>web</sup></sup> | ||
** | **GdmCl and urea concentration calculator from index of refraction. | ||
*[http://www.basic.northwestern.edu/biotools/oligocalc.html OligoCalc] Oligonucleotide Calculator <sup><sup>web</sup></sup> | |||
**Calculate a number of parameters for your nucleotide polymers | |||
*[http://www.physics.csbsju.edu/stats/ Statistics to use] from Saint John's University. <sup><sup>web</sup></sup> | |||
===<span id="DNA"></span>DNA=== | |||
*[http://www.affymetrix.com/estore/partners_programs/programs/developer/tools/affytools.affx#1_2 Affymetrix Tools] <sup><sup>software</sup></sup> | |||
**Microchip and SNP analysis software. [http://www.affymetrix.com/estore/partners_programs/programs/developer/tools/devnettools.affx#1_1 DevNet Tools] and [http://www.affymetrix.com/estore/partners_programs/genechip_compatible/genechip_compatible.affx#1_1 other compatible programs] also listed for download and use | |||
*[http://www.sanger.ac.uk/Software/Artemis/ Artemis] by the Sanger Center <sup><sup>software</sup></sup> | |||
**A free DNA sequence viewer and annotation tool (Java based). The Sanger Center also develops a number of other [http://www.sanger.ac.uk/resources/software/#t_alldownloads miscellaneous tools] for download | |||
*[http://www.mbio.ncsu.edu/BioEdit/bioedit.html BioEdit] <sup><sup>software</sup></sup> | |||
**Windows-only sequence alignment editor (no longer maintained, but free to download) | |||
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST] <sup><sup>web</sup></sup> | |||
**Finds regions of similarity between biological sequences. | |||
*[http:// | *[http://www.clcbio.com/products/clc-sequence-viewer/ CLC Sequence Viewer] <sup><sup>software</sup></sup> | ||
** | **Software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, graphical viewing, and output options. | ||
*[http:// | *[http://54.235.254.95/gd/index.html Gene Design] by Boeke lab <sup><sup>web</sup></sup> | ||
**Collection of online tools for codon optimization and shuffling, restriction site editing, and so on. | **Collection of online tools for codon optimization and shuffling, restriction site editing, and so on. | ||
*[http:// | *[http://www.dna20.com/tools/genedesigner.php GeneDesigner] by DNA2.0 <sup><sup>software</sup></sup> | ||
** | **Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail. | ||
** | **Free to download and works on Mac or PC. User agreement is somewhat restrictive, i.e. you cannot sell genes designed using the tool without permission. | ||
* | |||
** | *[http://genewarrior.com/ GeneWarrior] <sup><sup>web</sup></sup> | ||
**Free/simple online toolset for sequence manipulation | |||
*[http://genomecompiler.com/ Genome Compiler] <sup><sup>web</sup></sup> <sup><sup>software</sup></sup> | |||
**The Complete set of tools for sequence viewing, annotation and alignment. Free online & downloadable and supports all file formats | |||
*[http://www.idtdna.com/pages/scitools IDT SciTools] <sup><sup>web</sup></sup> | |||
**A number of web tools and calculators to assist in the design and execution of molecular biology research | |||
*[http://www.jalview.org/ Jalview] <sup><sup>software</sup></sup> | |||
**Program for multiple sequence alignment editing, visualization, and analysis | |||
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] by New England Biolabs, Inc. | *[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] by New England Biolabs, Inc. <sup><sup>web</sup></sup> | ||
**Tool for finding restriction sites, et cetera. | **Tool for finding restriction sites, et cetera. | ||
*[http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Primer3] | *[http://perlprimer.sourceforge.net/download.html PerlPrimer] <sup><sup>software</sup></sup> | ||
**Open source PCR primer design. Written in Perl/Tk. | |||
*[http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Primer3] <sup><sup>web</sup></sup> | |||
** Tool that lets you pick & evaluate primers from a DNA sequence | ** Tool that lets you pick & evaluate primers from a DNA sequence | ||
*[http://nihserver.mbi.ucla.edu/RACC/ Rare Codon Calculator (RaCC)] by NIH MBI Laboratory for Structural Genomics and Proteomics | *[http://qiime.org/ QIIME] (Quantitative Insights Into Microbial Ecology) <sup><sup>software</sup></sup> | ||
**Powerful suite of open source bioinformatics tools for performing microbiome analysis from raw sequences. | |||
*[http://nihserver.mbi.ucla.edu/RACC/ Rare Codon Calculator (RaCC)] by NIH MBI Laboratory for Structural Genomics and Proteomics <sup><sup>web</sup></sup> | |||
** Finds rare codons in a coding sequence. | ** Finds rare codons in a coding sequence. | ||
*[http://molbiol.edu.ru/eng/scripts/01_11.html Search of rare codons in nucleotide sequence] by "Practical Molecular Biology" | *[http://molbiol.edu.ru/eng/scripts/01_11.html Search of rare codons in nucleotide sequence] by "Practical Molecular Biology" <sup><sup>web</sup></sup> | ||
*[http://genome.nci.nih.gov/tools/reformat.html Sequence file format converter] from NIH <sup><sup>web</sup></sup> | |||
**Web tool for converting between sequence file formats. | |||
*[http://bioinformatics.org/sms/index.html Sequence Manipulation Suite] <sup><sup>web</sup></sup> | |||
**Quickly access a host of tools for analyzing and manipulating DNA, RNA, and protein sequences | |||
*[http://genomics.ucdavis.edu/benham/sidd/index.php SIDD] | *[http://genomics.ucdavis.edu/benham/sidd/index.php SIDD] <sup><sup>web</sup></sup> | ||
** Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA. | ** Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA. | ||
*[http://www.bioinfo.rpi.edu/applications/hybrid/download.php UNAFold] | *[http://www.bioinfo.rpi.edu/applications/hybrid/download.php UNAFold] <sup><sup>web</sup></sup> | ||
** Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also. | ** Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also. | ||
===RNA=== | *[http://www.drive5.com/software.html USEARCH] <sup><sup>software</sup></sup> | ||
* [http://www. | **High throughput sequence analysis (orders of magnitude faster than BLAST) and other software tools | ||
===<span id="RNA"></span>RNA=== | |||
* [http://www.genomecompiler.com/?utm_source=refferal_website&utm_medium=referral&utm_term=digital_tools_and_resources_rna&utm_content=website&utm_campaign=openwetware RBS Calculator in Genome Compiler] | |||
** Control translation initiation rate and predict protein production levels. | |||
*[http://mfold.rit.albany.edu/?q=DINAMelt/software UNAfold] by Michael Zuker. | * [http://www.fruitfly.org/seq_tools/promoter.html Promoter prediction] <sup><sup>web</sup></sup> | ||
**both prokaryote and eukaryotic promoter prediction | |||
*[http://mfold.rit.albany.edu/?q=DINAMelt/software UNAfold] by Michael Zuker. <sup><sup>web</sup></sup> | |||
**Apps for predicting RNA and DNA folds, calculating Tm's and free energies. Runs mfold + UNAfold servers | **Apps for predicting RNA and DNA folds, calculating Tm's and free energies. Runs mfold + UNAfold servers | ||
* [http://www.bioinfo.rpi.edu/applications/sfold/index.pl Sfold] | * [http://www.bioinfo.rpi.edu/applications/sfold/index.pl Sfold] <sup><sup>web</sup></sup> | ||
**Statistical Folding and Rational Design of Nucleic Acids. Predicts accessible RNA sites | |||
*[http://www.tbi.univie.ac.at/~ivo/RNA/ Vienna RNA] software | *[http://www.tbi.univie.ac.at/~ivo/RNA/ Vienna RNA] <sup><sup>software</sup></sup> | ||
**RNA secondary structure prediction and design | |||
===Protein=== | * [http://rna.ucsc.edu/rnacenter/xrna/xrna.html XRNA] <sup><sup>software</sup></sup> | ||
*[http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html AGADIR] by Serrano lab | **Java tools for creating RNA secondary structure diagrams | ||
===<span id="Protein"></span>Protein=== | |||
* [http://www.genomecompiler.com/?utm_source=refferal_website&utm_medium=referral&utm_term=digital_tools_and_resources_protein&utm_content=website&utm_campaign=openwetware RBS Calculator in Genome Compiler] | |||
** Control translation initiation rate and predict protein production levels | |||
*[http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html AGADIR] by Serrano lab <sup><sup>web</sup></sup> | |||
**An algorithm to predict the helical content of peptides. | **An algorithm to predict the helical content of peptides. | ||
*[http:// | *[http://keatingweb.mit.edu/avid/ AVID] by Keating lab <sup><sup>web</sup></sup> | ||
**An integrative framework for discovering functional relationships among proteins. | **An integrative framework for discovering functional relationships among proteins. | ||
*[http://dunbrack.fccc.edu/ | *[http://dunbrack.fccc.edu/bbdep2010/ Backbone-dependent rotamer library] by Dunbrack lab <sup><sup>web</sup></sup> | ||
**Libraries of sidechain rotamer from protein structures | **Libraries of sidechain rotamer from protein structures | ||
*[http://ncbi.nih.gov/Structure/CN3D/cn3d.shtml Cn3D] by NCBI | *[http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Cn3D] by NCBI <sup><sup>web</sup></sup> | ||
**A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView. | **A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView. | ||
*[http:// | *[http://www.bakerlab.org/contact_order/ Contact Order Calulator] by Baker lab <sup><sup>web</sup></sup> | ||
**Calculator to determine a protein's contact order | **Calculator to determine a protein's contact order | ||
*[http://us.expasy.org/ ExPASy Proteomics server] by the Swiss Institute of Bioinformatics | *[http://kinemage.biochem.duke.edu/software/dang.php Dang] by Richardsons' lab <sup><sup>software</sup></sup> | ||
**A command-line tool that generates a table of several useful geometric measurements for each residue or base from a PDB file. | |||
*[http://www.expasy.org/spdbv/ DeepView] by GlaxoSmithKline & Swiss Institute of Bioinformatics <sup><sup>software</sup></sup> | |||
**Awesome program for viewing and studying protein structure. | |||
*[http://us.expasy.org/ ExPASy Proteomics server] by the Swiss Institute of Bioinformatics <sup><sup>web</sup></sup> | |||
**Collection of links to many pages to calculate parameters of your favorite proteins | **Collection of links to many pages to calculate parameters of your favorite proteins | ||
*#[http://sosnick.uchicago.edu/pi_tool.html Compute pI/Mw] | *#[http://sosnick.uchicago.edu/pi_tool.html Compute pI/Mw] | ||
Line 174: | Line 386: | ||
*#*Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence. | *#*Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence. | ||
*[http:// | *[http://curie.utmb.edu/getarea.html GETAREA] by Sealy Center for Structural Biology <sup><sup>web</sup></sup> | ||
**Solvent accessible surface areas, atomic solvation energies, and their gradients for macromolecules | **Solvent accessible surface areas, atomic solvation energies, and their gradients for macromolecules | ||
*[http://paircoil2.csail.mit.edu/ PAIRCOIL2] by Keating and Berger labs | *[http://www.metazome.net/ Metazome] <sup><sup>web</sup></sup> | ||
**Proteome-level phylogeny and genomics | |||
*[http://salilab.org/modeller/ Modeller] by Sali lab <sup><sup>software</sup></sup> | |||
**Program for homology or comparative modeling of protein three-dimensional structures by satisfaction of spatial restraints. | |||
*[http://paircoil2.csail.mit.edu/ PAIRCOIL2] by Keating and Berger labs <sup><sup>web</sup></sup> | |||
**Tool to predict the parallel coiled coil fold from sequence using pairwise residue probabilities. | **Tool to predict the parallel coiled coil fold from sequence using pairwise residue probabilities. | ||
*[http://prospector.ucsf.edu/ ProteinProspector] by UCSF Mass Spectrometry Facility | *[http://prospector.ucsf.edu/ ProteinProspector] by UCSF Mass Spectrometry Facility <sup><sup>web</sup></sup> | ||
**Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments. | **Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments. | ||
*[http:// | *[http://pymol.sourceforge.net/ PyMOL] <sup><sup>software</sup></sup> | ||
** | **Molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. The latest version does not run on OSX 10.3. (from [[User:Kathmc | Kathleen]]). | ||
*[http://www.ks.uiuc.edu/Research/vmd/ VMD] by Theoretical and Computational Biophysics Group at UIUC <sup><sup>software</sup></sup> | |||
*[http://www. | **Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Generates pretty high resolution pictures of protein structures. | ||
*[http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php Zinc Finger Tools] by Barbas lab <sup><sup>web</sup></sup> | |||
*[http://www. | **Design Zinc Finger DNA binding proteins | ||
=== | ===<span id="Vectors"></span>Vectors=== | ||
*[http:// | *[http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] A plasmid Editor <sup><sup>software</sup></sup> | ||
** | **Simple tools for plasmid design and manipulation | ||
*[http://www.dna20.com/resources/genedesigner GeneDesigner] by DNA 2.0 <sup><sup>software</sup></sup> | |||
*[http://www. | **Design genes ''de novo'' with a powerful and intuitive user interface | ||
** | |||
*[http:// | *[http://genomecompiler.com/ Genome Compiler] <sup><sup>web</sup></sup> <sup><sup>software</sup></sup> | ||
** | **A free all-in-one platform for intuitive vector design and automatic assembly. Supports main construction techniques, manual and auto sequence annotation, alignment, primer design and compatible to all file formats. | ||
*[http://j5.jbei.org j5, DeviceEditor, and VectorEditor] <sup><sup>web</sup></sup> | |||
*[http:// | ** j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods | ||
** | ** DeviceEditor: a visual DNA design canvas that serves as front-end for j5 | ||
** VectorEditor: a visual DNA editing and annotation tool | |||
*[http:// | *[http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper] <sup><sup>web</sup></sup> | ||
** | **Generates and annotates a plasmid map based on sequence data | ||
*[http:// | *[http://serialbasics.free.fr/Serial_Cloner.html Serial Cloner] <sup><sup>software</sup></sup> | ||
** | **Light and intuitive tools for diverse molecular biology manipulations | ||
*[http:// | *[http://www.snapgene.com/products/snapgene_viewer/ SnapGene Viewer] <sup><sup>software</sup></sup> | ||
**Free version of [http://www.snapgene.com/ SnapGene]. Allows mapping of DNA up to 1 Gb in length. Convenient viewing and annotation tools for genetic constructs. | |||
*[http://www.lifetechnologies.com/us/en/home/life-science/cloning/vector-nti-software.html Vector NTI] <sup><sup>software</sup></sup> | |||
*[http:// | **Powerful but expensive vector editor. Supports most sequence types and easily manipulates genetic constructs. | ||
** | |||
*[http://www. | ===<span id="Writing/Composition/Organization"></span>Writing/Composition/Organization=== | ||
** | *[http://www.cambridgesoft.com/ CambridgeSoft] <sup><sup>software</sup></sup> | ||
**Numerous proprietary applications for research and composition (ChemBioDraw is usually accessible via academic institution email) | |||
*[http:// | *[http://coredemia.com/ Coredemia] <sup><sup>web</sup></sup> | ||
** | **Community for sharing and discussion of research papers | ||
*[http://docs.google.com/ Google Documents] by [http://www.google.com Google] | *[http://docs.google.com/ Google Documents] by [http://www.google.com Google] <sup><sup>web</sup></sup> | ||
** | **Sharable, web-based word processing, spreadsheets, and presentations | ||
*[http://evernote.com/ Evernote] <sup><sup>software</sup></sup> <sup><sup>app</sup></sup> | |||
**Powerful cross-platform note-taking, composition, and organization with cloud syncing. | |||
*[http://www.instagrok.com/ InstaGrok] <sup><sup>software</sup></sup> | |||
**Tool for seeking, collecting, and mapping information | |||
*[http://inkscape.org/en/ Inkscape] <sup><sup>web</sup></sup> | |||
**Free, feature-rich drawing program with support for SVG and PDF images | |||
*[http://www.mendeley.com/ Mendeley] <sup><sup>software</sup></sup> <sup><sup>app</sup></sup> | |||
*[http://www. | **Powerful and straightforward local and cloud-based reference manager | ||
** | |||
*[http://www.originlab.com/ Origin] <sup><sup>software</sup></sup> | |||
*[http:// | **Scientific graphing and data analysis software | ||
** | |||
*[ | *[http://www.qiqqa.com/ Qiqqa] <sup><sup>software</sup></sup> | ||
** | **Organize, annotate, search, and cite references from a PDF library (loads of extra features) | ||
*[http://www.readcube.com/ ReadCube] <sup><sup>software</sup></sup> | |||
* [http:// | **Reference manager, similar to Mendeley or Evernote. Can enhance PDFs and search PubMed from within the app. | ||
*[http://online.thinkfree.com/ ThinkFree Office Online] by ThinkFree <sup><sup>web</sup></sup> | |||
*[http:// | **Beta suite of office applicatins offered over the web | ||
** | |||
*[http:// | *[http://app.vesselsci.com/#!/accounts/login Vessel] <sup><sup>web</sup></sup> <sup><sup>app</sup></sup> | ||
** | **Digital lab notebook for organizing and sharing experiments, findings, protocols, and more. | ||
*[http:// | *[http://www.writeboard.com/ WriteBoard] by 37signals <sup><sup>web</sup></sup> | ||
** | **Permits writing of shareable, web-based text documents | ||
*[http:// | *[http://www.writely.com/ Writely] by Upstartle, LLC. <sup><sup>web</sup></sup> | ||
**A beta word processor run over the web | |||
** | |||
*[http://sheet.zoho.com/ Zoho] <sup><sup>web</sup></sup> | |||
*[http:// | **Sharable, web-based word processing, spreadsheets, and presentations (alternative to Google Docs) | ||
** | |||
=== | ==See also:== | ||
===[[Vectors]] - info/links related to cloning vectors.=== | |||
===[[Searching the literature]] - info/links on searching the scientific literature.=== | |||
===[[Synthetic Biology]] - info/links on Synthetic Biology.=== | |||
[[Category:DNA]] | |||
[[Category:RNA]] | |||
[[Category:Protein]] | |||
[[Category:Literature]] | |||
[[Category:Software]] | |||
[[Category:Cloning]] | |||
[[Category:Databases]] | |||
[[Category:Genomics]] | |||
[[Category:Protocol]] |
Latest revision as of 12:34, 26 January 2017
How to use this page
Please help us by adding new digital resources useful to the community here. Keep this page organized by following the
format and alphabetical organization already in place.
All of the links below are organized first by whether they are general reference or a more specified research tool.
The sub-categories are organized alphabetically by research topic. Note that many of the tools listed may fit into
multiple categories, but are only listed once. Tools of this type may be tagged with other relevant categories by
adding a link to another section of the page after the description. Use the *link format of the following DNA example:
QIIME (Quantitative Insights Into Microbial Ecology) software
Powerful suite of open source bioinformatics tools for performing microbiome analysis from raw sequences. *RNA
This allows for quick navigation around the page and the use of the * in Ctrl + F searches to differentiate between
sections and page body content.
Please help keep this page up to date by fixing old or broken links and by deleting listings that no longer work. If
you think that an item has been placed in the wrong category, feel free to move it. Please be cautious when downloading
software, and make sure to help the community by removing links with harmful content. Content with questionable scientific
value should also be removed.
All information resources are assumed to be online, but research tools should be tagged with web for online resources, software
for downloadable items, and app for items used on phones and tablets. Please tag any additional categories in this
way if needed. Additional suggestions for format changes may be executed directly or discussed on the talk page.
Information resources
References, texts, and information resources.
Databases
Search engines and data repositories. There are thousands available (see MetaBase). The few items listed here are some of the broadest and most powerful
General Search/Reference
- BioNumbers
- The database of useful biological numbers. (link to database)
- CDC Disease Conditions
- Filtered index of diseases from the CDC database
- EMBL-EBI
- Hugely extensive collection of resources, databases, and tools related to diverse aspects of bioinformatics and molecular biology, often containing everything one might need
- Entrez (NCBI)
- Search all NCBI databases
- MetaBase
- The database of biological databases - External link
- Tree of Life
- Collaborative encyclopedia of biodiversity
- Wolfram Alpha
- Computational server for finding/calculating summary data about a wide range of topics, plus useful widgets like reagent tables and gene lookup
Genome and Metabolism
- BioCyc
- Collection of thousands of pathway/genome databases for many organisms, plus software tools for understanding their data
- Colibri by Institut Pasteur
- E. coli genome browser; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the E. coli genome.
- EcoGene
- Database of all E. coli genes and sequences (Entrez data is pulled from here)
- EcoCyc
- Comprehensive biochemical pathway and gene function site for E. coli
- ENCODE
- Parts list for functional elements in the human genome
- Ensembl
- Eukaryotic genome browser
- Ensembl Genome
- Sister to Ensembl, not limited to Eukaryotes
- Inventory of Composable Elements (ICE) - The public instance of the JBEI Registry
- A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
- A site where you can explore the various features of the JBEI Registry software, and even get some work done!
- Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
- Follow a link to the underlying open-source software source code.
- KEGG
- Genomic database geared towards high-level functions of the biological system
- Mammalian Gene Collection
- Access to sequence-validated, full-length, protein-coding, mammalian cDNA clones
- MetaCyc
- Multi-organismal member of BioCyc collection; catalogs entire universe of metabolism
- SGD
- Saccharomyces genome database (yeast genome)
- UCSC Genome Bioinformatics
- Sequence reference for a large number of genomes
Protein
- Antibody Resource
- Enter a protein to search for antibodies and ELISA kits
- BRENDA
- Comprehensive enzyme information system
- ConSurf
- Server for the identification of functional regions in proteins
- Genome3D
- Consensus structural annotations and 3D models for sequences of model organisms (built upon numerous other useful related resources)
- Technical suppport on protein crystallization by Hampton Research
- Focused on protein crystallization but contains a lot of generally useful information about various reagents with respect to proteins.
- UniProt
- Extensive database of protein sequence and functional information
RNA
- Appendix by Ambion, Inc.
- Website with many useful nucleic acid parameters.
- GreenGenes
- 16S rRNA database and workbench (most recently updated data can be downloaded here)
- Ribosomal Database Project
- Quality-controlled, aligned and annotated Bacterial and Archaeal 16S rRNA sequences, and Fungal 28S rRNA sequences, and a suite of analysis tools
- SILVA
- Massive, searchable rRNA database (especially strong for microbes)
Vectors
- Addgene's Vector DB
- Addgene is a a non-profit plasmid repository where scientists can archive and share their plasmids. Addgene assists with data submission and all tech transfer issues. Plasmids can be requested from Addgene for a fee to cover expenses.
- AddGene Vectors can be directly imported into Genome Compiler software platform, in which you can easily edit and visualize it.
Lab Techniques
- Barrick Lab of UT Austin
- Tons of helpful resources like protocols, guides, links, and tools for lab work
- BenchFly
- Search, view, upload, create, and host scientific protocol videos
- Current Protocols in Molecular Biology
- Handbook of protocols. (Links to Wiley Online Library)
- Gene expression in E. coli by Ehrmann lab
- Tips and information on gene expression in E. coli
- Molecular Cloning by Sambrook and Russell
- Handbook of protocols. Subscription only. External link
- OWW Materials
- Useful information for making or obtaining reagents, enzymes, buffers, etc.
- On Being a Scientist by National Academy of Science
- NAS report on responsible conduct in research.
- OWW Protocols
- Growing collection of laboratory protocols and techniques
- Polony Protocols by Church and Mitra Lab
- Polonies are colonies of PCR amplicons derived from a single molecule of nucleic acid.
- Protocol-online by Dr. Long-Cheng Li
- A database of research protocols in a variety of life science fields. It has a popular discussion forum.
- Protocols.io app web
- Huge, open access life science protocol repository for discovery and sharing of scientific methods
- VADLO Search Engine
- VADLO is a search engine for Life Sciences Protocols, Online Tools, Databases, Software, and Biomedical Powerpoint Lectures. It also has Daily research cartoons, called *"Life in Research" Cartoons.
Microbial physiology
- CyberCell Database (CCDB) by Institute for Biomolecular Design
- Several tables describing statistical data on E. coli compiled from several sources.
- EcoSal by ASM Press
- An incomplete web version of the publication Escherichia coli and Salmonella: Cellular and Molecular Biology. (Subscription required)
- Metabolic Pathways Poster PDF by SigmaAldrich
- Free digital version of the paper Metabolic Pathways map. Because it is a PDF, it is also searchable.
- MicrobeWiki
- Student edited resource on microbes and microbiology (curated pages reviewed by microbiologists)
Teaching
- Khan Academy (Biology)
- Selection of science videos and short courses, including the popular Crash Course series
- PhET
- Interactive simulations for science and math
- ScienceHack
- Search engine for science videos with a review system
Research Tools
Tools and applications to aid in research tasks.
General
- Benchling web
- Online apps for cloning, molecular biology, and analysis
- Bioinformatics Toolbox from DNA2.0 web
- Contains many Javascript tools to do common tasks.
- Cancer Genome Anatomy Project web
- Resources and tools related to the characterization of cancer gene expression profiles
- Experiment web
- Crowdfunded scientific research
- Genome Compiler web software
- A powerful, free online & downloadable genetic engineering all-in-one platform for molecular & synthetic biologists
- FastPCR software
- An integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching
- Galaxy web
- Easy-to-use Bioinformatics manipulation tools for UCSC data
- iGEM Parts Registry web
- Formerly curated by MIT, this is an open repository of BioBricks; the place for all your standard biological parts.
- Ingeneue by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at the Center for Cell Dynamics software
- An open-source java program for modeling gene regulatory networks. Users can rapidly build networks by specifying their topology, initial conditions, connectivity, and known parameters. Ingeneue can then search/explore paramter space for desired behavior, simulate the effects of noise and mutation, and generate statistics/time graphs of the system.
- MABL web
- Reconstruct and analyze phylogenetic relationships between molecular sequences
- OpenCFU software
- Local cell colony counting software
- MCDS software
- All-in-one molecular cloning and genetic engineering design, simulation & management tool for complex synthetic biology and metabolic engineering project.
- PaR-PaR Laboratory Automation Platform web
- PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour.
- Pinecone by Serotiny web
- High-level design, analysis and transmission of protein constructs. Pinecone matches users' designs with CRO's or DNA synthesizers to produce genetic starting material (dsDNA, plasmid or purified protein). Facilitates mutation and combinatorial protein sets that benefit from manufacturing economies of scale.
- PubChase software app
- Generates research article recommendations unique to each user. Site also has a special academic community.
- Science Gateway web
- Collection of science-related links, including links to journals, catalogs, and tools. See their about page.
Calculators
- [GdmCl] and [Urea] from refractive index by Sosnick lab web
- GdmCl and urea concentration calculator from index of refraction.
- OligoCalc Oligonucleotide Calculator web
- Calculate a number of parameters for your nucleotide polymers
- Statistics to use from Saint John's University. web
DNA
- Affymetrix Tools software
- Microchip and SNP analysis software. DevNet Tools and other compatible programs also listed for download and use
- Artemis by the Sanger Center software
- A free DNA sequence viewer and annotation tool (Java based). The Sanger Center also develops a number of other miscellaneous tools for download
- BioEdit software
- Windows-only sequence alignment editor (no longer maintained, but free to download)
- BLAST web
- Finds regions of similarity between biological sequences.
- CLC Sequence Viewer software
- Software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, graphical viewing, and output options.
- Gene Design by Boeke lab web
- Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
- GeneDesigner by DNA2.0 software
- Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail.
- Free to download and works on Mac or PC. User agreement is somewhat restrictive, i.e. you cannot sell genes designed using the tool without permission.
- GeneWarrior web
- Free/simple online toolset for sequence manipulation
- Genome Compiler web software
- The Complete set of tools for sequence viewing, annotation and alignment. Free online & downloadable and supports all file formats
- IDT SciTools web
- A number of web tools and calculators to assist in the design and execution of molecular biology research
- Jalview software
- Program for multiple sequence alignment editing, visualization, and analysis
- NEB Cutter by New England Biolabs, Inc. web
- Tool for finding restriction sites, et cetera.
- PerlPrimer software
- Open source PCR primer design. Written in Perl/Tk.
- Primer3 web
- Tool that lets you pick & evaluate primers from a DNA sequence
- QIIME (Quantitative Insights Into Microbial Ecology) software
- Powerful suite of open source bioinformatics tools for performing microbiome analysis from raw sequences.
- Rare Codon Calculator (RaCC) by NIH MBI Laboratory for Structural Genomics and Proteomics web
- Finds rare codons in a coding sequence.
- Search of rare codons in nucleotide sequence by "Practical Molecular Biology" web
- Sequence file format converter from NIH web
- Web tool for converting between sequence file formats.
- Sequence Manipulation Suite web
- Quickly access a host of tools for analyzing and manipulating DNA, RNA, and protein sequences
- SIDD web
- Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA.
- UNAFold web
- Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.
- USEARCH software
- High throughput sequence analysis (orders of magnitude faster than BLAST) and other software tools
RNA
- RBS Calculator in Genome Compiler
- Control translation initiation rate and predict protein production levels.
- Promoter prediction web
- both prokaryote and eukaryotic promoter prediction
- UNAfold by Michael Zuker. web
- Apps for predicting RNA and DNA folds, calculating Tm's and free energies. Runs mfold + UNAfold servers
- Sfold web
- Statistical Folding and Rational Design of Nucleic Acids. Predicts accessible RNA sites
- Vienna RNA software
- RNA secondary structure prediction and design
- XRNA software
- Java tools for creating RNA secondary structure diagrams
Protein
- RBS Calculator in Genome Compiler
- Control translation initiation rate and predict protein production levels
- AGADIR by Serrano lab web
- An algorithm to predict the helical content of peptides.
- AVID by Keating lab web
- An integrative framework for discovering functional relationships among proteins.
- Backbone-dependent rotamer library by Dunbrack lab web
- Libraries of sidechain rotamer from protein structures
- Cn3D by NCBI web
- A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView.
- Contact Order Calulator by Baker lab web
- Calculator to determine a protein's contact order
- Dang by Richardsons' lab software
- A command-line tool that generates a table of several useful geometric measurements for each residue or base from a PDB file.
- DeepView by GlaxoSmithKline & Swiss Institute of Bioinformatics software
- Awesome program for viewing and studying protein structure.
- ExPASy Proteomics server by the Swiss Institute of Bioinformatics web
- Collection of links to many pages to calculate parameters of your favorite proteins
- Compute pI/Mw
- A tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot and/or TrEMBL entries or for user entered sequences.
- ProtParam
- A tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence.
- Translate
- Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
- GETAREA by Sealy Center for Structural Biology web
- Solvent accessible surface areas, atomic solvation energies, and their gradients for macromolecules
- Metazome web
- Proteome-level phylogeny and genomics
- Modeller by Sali lab software
- Program for homology or comparative modeling of protein three-dimensional structures by satisfaction of spatial restraints.
- PAIRCOIL2 by Keating and Berger labs web
- Tool to predict the parallel coiled coil fold from sequence using pairwise residue probabilities.
- ProteinProspector by UCSF Mass Spectrometry Facility web
- Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments.
- PyMOL software
- Molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. The latest version does not run on OSX 10.3. (from Kathleen).
- VMD by Theoretical and Computational Biophysics Group at UIUC software
- Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Generates pretty high resolution pictures of protein structures.
- Zinc Finger Tools by Barbas lab web
- Design Zinc Finger DNA binding proteins
Vectors
- ApE A plasmid Editor software
- Simple tools for plasmid design and manipulation
- GeneDesigner by DNA 2.0 software
- Design genes de novo with a powerful and intuitive user interface
- Genome Compiler web software
- A free all-in-one platform for intuitive vector design and automatic assembly. Supports main construction techniques, manual and auto sequence annotation, alignment, primer design and compatible to all file formats.
- j5, DeviceEditor, and VectorEditor web
- j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods
- DeviceEditor: a visual DNA design canvas that serves as front-end for j5
- VectorEditor: a visual DNA editing and annotation tool
- PlasMapper web
- Generates and annotates a plasmid map based on sequence data
- Serial Cloner software
- Light and intuitive tools for diverse molecular biology manipulations
- SnapGene Viewer software
- Free version of SnapGene. Allows mapping of DNA up to 1 Gb in length. Convenient viewing and annotation tools for genetic constructs.
- Vector NTI software
- Powerful but expensive vector editor. Supports most sequence types and easily manipulates genetic constructs.
Writing/Composition/Organization
- CambridgeSoft software
- Numerous proprietary applications for research and composition (ChemBioDraw is usually accessible via academic institution email)
- Coredemia web
- Community for sharing and discussion of research papers
- Google Documents by Google web
- Sharable, web-based word processing, spreadsheets, and presentations
- Evernote software app
- Powerful cross-platform note-taking, composition, and organization with cloud syncing.
- InstaGrok software
- Tool for seeking, collecting, and mapping information
- Inkscape web
- Free, feature-rich drawing program with support for SVG and PDF images
- Mendeley software app
- Powerful and straightforward local and cloud-based reference manager
- Origin software
- Scientific graphing and data analysis software
- Qiqqa software
- Organize, annotate, search, and cite references from a PDF library (loads of extra features)
- ReadCube software
- Reference manager, similar to Mendeley or Evernote. Can enhance PDFs and search PubMed from within the app.
- ThinkFree Office Online by ThinkFree web
- Beta suite of office applicatins offered over the web
- Vessel web app
- Digital lab notebook for organizing and sharing experiments, findings, protocols, and more.
- WriteBoard by 37signals web
- Permits writing of shareable, web-based text documents
- Writely by Upstartle, LLC. web
- A beta word processor run over the web
- Zoho web
- Sharable, web-based word processing, spreadsheets, and presentations (alternative to Google Docs)