Lidstrom:Back Door:Useful Links

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Protein Tools)
(Protein Tools)
Line 89: Line 89:
*[http://www.cgl.ucsf.edu/chimera/download.html Chimera]
*[http://www.cgl.ucsf.edu/chimera/download.html Chimera]
-
Structure Prediction
+
==== Structure Prediction ====
*[http://swissmodel.expasy.org/ Swiss Model]
*[http://swissmodel.expasy.org/ Swiss Model]
*[http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index Phyre]
*[http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index Phyre]
-
Alignment
+
==== Alignment ====
*[http://fatcat.burnham.org/ FATCAT]
*[http://fatcat.burnham.org/ FATCAT]

Revision as of 13:26, 7 June 2014

Back to Back Door

Contents

General

  • general biology/biotech basics from Integrated DNA Technologies (IDT)
    • Molecular Biology Background:
      • Mitochondrial DNA, Mendelian Genetics, Molecular Facts and Figures, Protein Synthesis, microRNAs, DNA Replication, A Brief History of DNA, What is an Oligo
    • Molecular Biology Techniques:
      • The Polymerase Chain Reaction, Gel Electrophoresis , Restriction Endonucleases , DNA Sequencing , Antisense Technologies , A Basic PCR Protocol
  • Qiagen Bench Guide
    • cell culture & DNA

Microbiology

E. coli

Molecular Biology

DNA/RNA Tools

plasmid annotations

  • APE free plasmid editor
  • Serial Cloner free equivalent to Vector NTI
  • PlasMapper
    • The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format.

codon optimization

codon frequency tables for E. coli

other

  • Agarose gel electrophoresis basics
  • Genewiz DNA sequencing
  • IDT DNA oligos
  • EBI Sequence Alignment
  • BLAST! Sequence Alignment
    • The most commonly used nucleotide/protein alignment tool.
    • start here (animated web intro)
    • Practical intro: CHS protocols
      • protein alignments: "The line between the two sequences indicates the similarities between the sequences. If the query and the subject have the same amino acid at a given location, the residue itself is shown. Conservative substitutions, as judged by the substitution matrix, are indicated with +."
  • RBS strength calculator/engineering tool
    • Another: link
    • Accuracy stated by FAQ: "on average, the predictions of the RBS Calculator are accurate to within a factor of 2.3, equivalent to an error of 1.82 kcal/mol in the thermodynamic model. There is a 47% chance that a synthetic ribosome binding site will be accurate to within 2-fold of its predicted translation initiation rate." So you can estimate it to have accuracy within an order of magnitude. Pretty sensitive to the amount of upstream & downstream sequence info you provide. Check your forward engineering designs with more bp included in the reverse engineering mode.
  • Finnzyme Tm calculator: use if you use Phusion DNA polymerase
  • Finnzyme multiple primer analyzer looks for primer dimers (check before ordering primers)
  • Replicons and Compatibility
  • Nanodrop Info
  • NuPack Nucleic acid secondary structure predictor

BioBricks

Protein Tools

Size Estimation

Visualization

Pymol

Structure Prediction

==== Alignment ==== 

Enzymes

  • Databases:
    • Sabio-RK: biochemical reaction kinetics database
    • BRENDA: (BRaunschweig ENzyme DAtabase)

Synthetic Biology

Mass Spec

HPLC

  • Shimadzu Virtual Advisor.
    • Ask Nicole, Amanda, or Janet for the lab log-in.

Programming/Scripting

R

Regular expressions:

  • Rubular. Website to test regular expressions in Ruby, but works for grep in R. It is possible it works a little differently in Ruby and grep.

GitHub

Protein Engineering

Misc

Presentations/Posters

University of Washington

UW Resources

Safety/Lab Technique

Graphics

Statistics

Multiple linear regression

Misc

  • Mendeley : reference/paper manager that's awesome
    • Janet's workflow: (1) discover papers via google scholar saved search, (2) save them to Mendeley in the appropriate nested folder regardless of whether you intend to read it now or "some day when I'm thinking about that topic" (3) read in Mendeley, which makes a green dot (indicating unread) go away.
    • You can highlight and keep notes on top of your PDFs enabling quicker review of topics.
    • Imagine being able to query all of the papers you have ever read for a topic of interest! You can also see whether you have ever read a paper or not, potentially saving yourself time.
    • I also like the idea that I will never lose track of a paper I want to tell someone about. It isn't uncommon for someone to tell me about a paper but be unable to find it and send it to me. This should never happen for a dedicated Mendeley user.
  • Endy:Victor3_plate_reader/filters Filters for Fluorescence
  • Equilibrator
  • BioNumbers: a collection of useful bionumbers
  • emolecules Chemical Lookup
Personal tools