Sequence clustering: Difference between revisions

Revision as of 20:56, 9 May 2018

Revision as of 12:43, 11 May 2018

Line 54:

|pmid=11917018

|doi=10.1093/nar/30.7.1575 |pmc=101833}}</ref>

* BAG: a graph theoretic sequence clustering algorithm<ref>{{cite web |url=http://bio.informatics.indiana.edu/sunkim/BAG/ |title=Archived copy |accessdate=2004-02-19 |deadurl=yes |archiveurl=https://web.archive.org/web/20031206172749/http://bio.informatics.indiana.edu/sunkim/BAG/ |archivedate=2003-12-06 |df= }}</ref>

* JESAM:<ref>{{cite web|url=http://www.littlest.co.uk/software/bioinf/old_packages/jesam/jesam_paper.html|title=Bioinformatics Paper: JESAM: CORBA software components for EST alignments and clusters|work=littlest.co.uk}}</ref> Open source parallel scalable DNA alignment engine with optional clustering software component

* UICluster:<ref>http://ratest.eng.uiowa.edu/pubsoft/clustering/</ref> Parallel Clustering of EST (Gene) Sequences

Line 72:

* PATDB: a program for rapidly identifying perfect substrings

* nrdb:<ref>https://web.archive.org/web/20080101032917/http://blast.wustl.edu/pub/nrdb/</ref> a program for merging trivially redundant (identical) sequences

* CluSTr:<ref>{{cite web |url=http://www.ebi.ac.uk/clustr/ |title=Archived copy |accessdate=2006-11-23 |deadurl=yes |archiveurl=https://web.archive.org/web/20060924012903/http://www.ebi.ac.uk/clustr/ |archivedate=2006-09-24 |df= }}</ref> A single-linkage protein sequence clustering database from Smith-Waterman sequence similarities; covers over 7 mln sequences including UniProt and IPI

* ICAtools<ref>{{cite web|url=http://www.littlest.co.uk/software/bioinf/old_packages/icatools/|title=Introduction to the ICAtools|work=littlest.co.uk}}</ref> - original (ancient) DNA clustering package with many algorithms useful for artifact discovery or EST clustering

* Virus Orthologous Clusters:<ref>{{cite web|url=http://athena.bioc.uvic.ca/tools/VOCS|title=VOCS - Viral Bioinformatics Resource Center|work=uvic.ca}}</ref> A viral protein sequence clustering database; contains all predicted genes from eleven virus families organized into ortholog groups by BLASTP similarity