Difference between revisions of "Sequence analysis"
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==Integrated tools== | ==Integrated tools== | ||
+ | {{#pmid: 15215403}} | ||
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+ | {{#pmid: 23031578}} | ||
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{{#pmid:19389726}} | {{#pmid:19389726}} | ||
http://annie.bii.a-star.edu.sg | http://annie.bii.a-star.edu.sg | ||
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+ | http://smart.embl-heidelberg.de/ | ||
Revision as of 13:01, 28 October 2012
Sequence analysis
This page is a placeholder, or under current development; it is here principally to establish the logical framework of the site. The material on this page is correct, but incomplete.
Summary ...
Contents
Contents
Examples
Motifs
Disorder
Deng et al. (2012) A comprehensive overview of computational protein disorder prediction methods. Mol Biosyst 8:114-21. (pmid: 21874190) |
Kozlowski & Bujnicki (2012) MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics 13:111. (pmid: 22624656) |
Signal peptides
Bendtsen et al. (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783-95. (pmid: 15223320) |
Emanuelsson et al. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2:953-71. (pmid: 17446895) |
Petersen et al. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8:785-6. (pmid: 21959131) |
Secondary Structure
Pirovano & Heringa (2010) Protein secondary structure prediction. Methods Mol Biol 609:327-48. (pmid: 20221928) |
Coiled coils
Rackham et al. (2010) The evolution and structure prediction of coiled coils across all genomes. J Mol Biol 403:480-93. (pmid: 20813113) |
Transmembrane Helices
BENCHMARK OF MEMBRANE HELIX PREDICTIONS FROM SEQUENCE
Location
Repeats
Heger & Holm (2000) Rapid automatic detection and alignment of repeats in protein sequences. Proteins 41:224-37. (pmid: 10966575) |
http://www.ebi.ac.uk/Tools/pfa/radar/
Pellegrini et al. (2012) Ab initio detection of fuzzy amino acid tandem repeats in protein sequences. BMC Bioinformatics 13 Suppl 3:S8. (pmid: 22536906) |
Biegert & Söding (2008) De novo identification of highly diverged protein repeats by probabilistic consistency. Bioinformatics 24:807-14. (pmid: 18245125) |
http://toolkit.lmb.uni-muenchen.de/hhrepid
Integrated tools
Rost et al. (2004) The PredictProtein server. Nucleic Acids Res 32:W321-6. (pmid: 15215403) |
Cong & Grishin (2012) MESSA: MEta-Server for protein Sequence Analysis. BMC Biol 10:82. (pmid: 23031578) |
Ooi et al. (2009) ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res 37:W435-40. (pmid: 19389726) |
http://annie.bii.a-star.edu.sg
http://smart.embl-heidelberg.de/
Further reading and resources