Difference between revisions of "Sequence logo"
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*[http://www.ccrnp.ncifcrf.gov/~pnh/papers/poster/ucb.htm Visualizing DNA binding sites: Sequence Logos and Walkers] | *[http://www.ccrnp.ncifcrf.gov/~pnh/papers/poster/ucb.htm Visualizing DNA binding sites: Sequence Logos and Walkers] | ||
*[http://www.lecb.ncifcrf.gov/~toms/logoprograms.html How Can I Make Sequence Logos on My Own Computer?] | *[http://www.lecb.ncifcrf.gov/~toms/logoprograms.html How Can I Make Sequence Logos on My Own Computer?] | ||
| + | *[http://arep.med.harvard.edu/ecoli_matrices/ E. coli DNA-Binding Site Matrices Applied to the Complete E. coli K12 Genome] | ||
| + | *[http://clcbio.com/index.php?id=869 Sequence logo] — by CLC bio | ||
| + | *[http://publib.boulder.ibm.com/infocenter/db2luw/v9/index.jsp?topic=/com.ibm.websphere.ii.foundation.conn.fw.lsu.doc/configuring/rlsucf01.html Codon frequency table format] | ||
| + | *[http://clcbio.com/index.php?id=43 Hydrophobicity scales] — by CLC bio | ||
===Tools=== | ===Tools=== | ||
*[http://weblogo.berkeley.edu/ WebLogo] — (Online) a web based application designed to make the generation of sequence logos as easy and painless as possible. | *[http://weblogo.berkeley.edu/ WebLogo] — (Online) a web based application designed to make the generation of sequence logos as easy and painless as possible. | ||
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*[http://biogenio.com/logo/ GENIO] (Online) | *[http://biogenio.com/logo/ GENIO] (Online) | ||
*[http://www.bionut.ki.se/groups/tbu/logobar/ LogoBar] (Java application) | *[http://www.bionut.ki.se/groups/tbu/logobar/ LogoBar] (Java application) | ||
| + | *[http://www.encorbio.com/protocols/Codon.htm Codon Optimization Calculator] | ||
| + | ===Databases=== | ||
| + | *[http://www.kazusa.or.jp/codon/ Codon Usage Database] — data generated from NCBI-GenBank Flat File Release 156.0 [2006-10-15]; 32,775 organisms. | ||
| + | *[http://www.genome.ad.jp/dbget/aaindex.html AAindex] — Amino acid indices and similarity matrices | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
[[Category:Graphics software]] | [[Category:Graphics software]] | ||
Latest revision as of 01:49, 4 August 2007
A sequence logo in bioinformatics is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA or RNA) or amino acids (in protein sequences).
To create sequence logos, related sequences—DNA, RNA, or protein sequences, or DNA sequences that have common conserved binding sites—are aligned so that the most conserved parts create good alignments. A sequence logo can then be created from the conserved multiple sequence alignment. The sequence logo will show how well residues are conserved at each position: the fewer the number of residues, the higher the letters will be, because the better the conservation is at that position. Different residues at the same position will be scaled according to their frequency. Sequence logos can be used to represent conserved DNA binding sites, where transcription factors bind.
References
- Schneider TD, Stephens RM (1990). "Sequence logos: a new way to display consensus sequences". Nucleic Acids Res, 18:6097–6100.
External links
- How to read sequence logos.
- WebLogo: A Sequence Logo Generator (Publication with fulltext access).
- PredictProtein
- A Gallery of Sequence Logos
- Visualizing DNA binding sites: Sequence Logos and Walkers
- How Can I Make Sequence Logos on My Own Computer?
- E. coli DNA-Binding Site Matrices Applied to the Complete E. coli K12 Genome
- Sequence logo — by CLC bio
- Codon frequency table format
- Hydrophobicity scales — by CLC bio
Tools
- WebLogo — (Online) a web based application designed to make the generation of sequence logos as easy and painless as possible.
- plogo — Protein Sequence Logos using Relative Entropy
- RNA Structure Logo
- GENIO (Online)
- LogoBar (Java application)
- Codon Optimization Calculator
Databases
- Codon Usage Database — data generated from NCBI-GenBank Flat File Release 156.0 [2006-10-15]; 32,775 organisms.
- AAindex — Amino acid indices and similarity matrices
