. 2005 Jul 1;33(Web Server issue):W274-6.
doi: 10.1093/nar/gki493.
SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs
Affiliations
- PMID: 15980468
- PMCID: PMC1160253
- DOI: 10.1093/nar/gki493
Item in Clipboard
SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs
Nucleic Acids Res.
.
Abstract
Establishment of similarities between proteins is very important for the study of the relationship between sequence, structure and function and for the analysis of evolutionary relationships. Motif-based search methods play a crucial role in establishing the connections between proteins that are particularly useful for distant relationships. This paper reports SCANMOT, a web-based server that searches for similarities between proteins by simultaneous matching of multiple motifs. SCANMOT searches for similar sequences in entire sequence databases using multiple conserved regions and utilizes inter-motif spacing as restraints. The SCANMOT server is available via http://www.ncbs.res.in/~faculty/mini/scanmot/scanmot.html.
Similar articles
-
iMOT: an interactive package for the selection of spatially interacting motifs.Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W602-5. doi: 10.1093/nar/gkh375. Nucleic Acids Res. 2004. PMID: 15215459 Free PMC article.
-
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns.Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W255-61. doi: 10.1093/nar/gki496. Nucleic Acids Res. 2005. PMID: 15980465 Free PMC article.
-
Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases.Bioinformatics. 2003 Jul 22;19(11):1381-90. doi: 10.1093/bioinformatics/btg164. Bioinformatics. 2003. PMID: 12874050
-
Identification of motifs in protein sequences.Curr Protoc Cell Biol. 2001 May;Appendix 1:Appendix 1C. doi: 10.1002/0471143030.cba01cs00. Curr Protoc Cell Biol. 2001. PMID: 18228275 Review.
-
Tools and resources for identifying protein families, domains and motifs.Genome Biol. 2002;3(1):REVIEWS2001. doi: 10.1186/gb-2001-3-1-reviews2001. Epub 2001 Dec 19. Genome Biol. 2002. PMID: 11806833 Free PMC article. Review.
Cited by
-
Recent trends in remote homology detection: an Indian Medley.Bioinformation. 2006 Feb 21;1(3):94-6. doi: 10.6026/97320630001094. Bioinformation. 2006. PMID: 17597865 Free PMC article.
-
iMOTdb--a comprehensive collection of spatially interacting motifs in proteins.Nucleic Acids Res. 2006 Jan 1;34(Database issue):D285-6. doi: 10.1093/nar/gkj125. Nucleic Acids Res. 2006. PMID: 16381866 Free PMC article.
-
Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.Proteins. 2008 May 1;71(2):631-40. doi: 10.1002/prot.21777. Proteins. 2008. PMID: 17972284 Free PMC article.
-
MegaMotifBase: a database of structural motifs in protein families and superfamilies.Nucleic Acids Res. 2008 Jan;36(Database issue):D218-21. doi: 10.1093/nar/gkm794. Epub 2007 Oct 11. Nucleic Acids Res. 2008. PMID: 17933773 Free PMC article.
-
MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences.Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W356-61. doi: 10.1093/nar/gkl309. Nucleic Acids Res. 2006. Corrected and republished in: Nucleic Acids Res. 2008 Mar;36(4):1400-6. doi: 10.1093/nar/gkm717. PMID: 16845025 Free PMC article. Corrected and republished.
References
-
- Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981;147:195–197. - PubMed
-
- Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410. - PubMed
-
- Altschul S.F., Gish W. Local alignment statistics. Methods Enzymol. 1996;266:460–480. - PubMed
