Chan:Bioinformatics Sites

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'''Chan Lab'''<br>
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<br>
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[http://www-plb.ucdavis.edu/ Department of Plant Biology], [http://www.ucdavis.edu/ UC Davis] and [http://www.hhmi.org HHMI]
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<div style="padding: .4em .9em .9em">
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[[Chan|Home]]
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----
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[[Chan:Research|Research]]
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[[Chan:Publications|Publications]]
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[[Chan:People|People]]
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[[Chan:Links|Links]]
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[[Chan:Bioinformatics Sites|Bioinformatics]]
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[[Chan:Contact|Contact]]
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<div style="padding: .4em .9em .9em">
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<b>Arabidopsis tools:</b><br>
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[http://www.arabidopsis.org/Blast/ TAIR BLAST search]<br>
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[http://tigrblast.tigr.org/er-blast/index.cgi?project=ath1 TIGR Arabidopsis BLAST Search]<br>
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[http://signal.salk.edu/cgi-bin/tdnaexpress Salk Institute Genome Analysis Laboratory (SIGnaL) T-DNA Express]<br>
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[http://signal.salk.edu/tdnaprimers.html Primer design for T-DNAs]<br>
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[http://www.psb.ugent.be/gateway/index.php Dirk Inze GATEWAY vectors]
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<b>Arabidopsis genome databases:</b><br>
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[http://www.arabidopsis.org/ TAIR (The Arabidopsis Information Resource)]<br>
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[http://www.arabidopsis.org/servlets/sv TAIR Seqviewer]<br>
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[http://atensembl.arabidopsis.info/index.html AtEnsembl]<br>
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[http://www.weigelworld.org/resources WeigelWorld Resources incl. AtGenExpress]<br>
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[http://mocklerlab.cgrb.oregonstate.edu/ Todd Mockler expression tools]<br>
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[http://epigenomics.mcdb.ucla.edu/DNAmeth/ Jacobsen/Ecker Arabidopsis Methylome Database]<br>
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[http://asrp.cgrb.oregonstate.edu/ Carrington Lab siRNA Database]<br>
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[http://mpss.udel.edu/at/ MPSS Small RNAs and Transcripts]<br>
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<b>Yeast Genome Databases:</b><br>
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[http://www.genedb.org/genedb/pombe/ ''S.pombe'' genome database]<br>
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[http://www.yeastgenome.org/ ''S.cerevisiae'' genome database]<br>
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<b>Bioinformatics:</b><br>
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[http://www.ncbi.nlm.nih.gov/ NCBI homepage]<br>
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[http://www.ncbi.nlm.nih.gov/blast/ BLAST at NCBI]<br>
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[http://www.ncbi.nlm.nih.gov/BLAST/Genome/PlantBlast.shtml BLAST Plant Genomes]<br>
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[http://smart.embl-heidelberg.de/ SMART Protein Domains]<br>
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[http://www.ebi.ac.uk/clustalw/ ClustalW at EBI]<br>
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[http://bibiserv.techfak.uni-bielefeld.de/dialign/submission.html Dialign multiple sequence alignment]<br>
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[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/ YOGY homolog search]<br>
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[http://inparanoid.sbc.su.se/cgi-bin/index.cgi Inparanoid homolog search]<br>
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[http://meme.nbcr.net/meme/intro.html MEME motif finder]<br>
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<b>Experimental:</b><br>
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[http://www3.interscience.wiley.com/browse/?type=CURRENT_PROTOCOL Current Protocols]<br>
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[http://frodo.wi.mit.edu/primer3/ Primer3]<br>
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[http://www.basic.northwestern.edu/biotools/oligocalc.html Oligo Calculator]<br>
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[http://rebase.neb.com/rebase/rebase.html REBase at NEB]<br>
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[http://helix.wustl.edu/dcaps/dcaps.html dCAPs Finder]<br>
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[http://www.fourmilab.ch/rpkp/experiments/analysis/chiCalc.html Chi-square calculator]<br>
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[http://www.proweb.org/coddle/ CODDLE for TILLING]<br>
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[http://www-rcf.usc.edu/~forsburg/#info Forsburg lab S.pombe methods]<br>
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----
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<b>Literature:</b><br>
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[http://www.ncbi.nlm.nih.gov/ NCBI]<br>
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[http://newisiknowledge.com ISI Knowledge]<br>
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[http://scholar.google.com/ Google Scholar]<br>
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<br>
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Current revision


Chan Lab

Department of Plant Biology, UC Davis and HHMI




Arabidopsis tools:
TAIR BLAST search
TIGR Arabidopsis BLAST Search
Salk Institute Genome Analysis Laboratory (SIGnaL) T-DNA Express
Primer design for T-DNAs
Dirk Inze GATEWAY vectors


Arabidopsis genome databases:
TAIR (The Arabidopsis Information Resource)
TAIR Seqviewer
AtEnsembl
WeigelWorld Resources incl. AtGenExpress
Todd Mockler expression tools
Jacobsen/Ecker Arabidopsis Methylome Database
Carrington Lab siRNA Database
MPSS Small RNAs and Transcripts


Yeast Genome Databases:
S.pombe genome database
S.cerevisiae genome database


Bioinformatics:
NCBI homepage
BLAST at NCBI
BLAST Plant Genomes
SMART Protein Domains
ClustalW at EBI
Dialign multiple sequence alignment
YOGY homolog search
Inparanoid homolog search
MEME motif finder


Experimental:
Current Protocols
Primer3
Oligo Calculator
REBase at NEB
dCAPs Finder
Chi-square calculator
CODDLE for TILLING
Forsburg lab S.pombe methods


Literature:
NCBI
ISI Knowledge
Google Scholar

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