Sequence clustering: Difference between revisions

Revision as of 00:24, 30 September 2018

Revision as of 01:25, 28 November 2018

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* CD-HIT<ref name=cdhit/>

* [[UCLUST]] in USEARCH<ref name=usearch/>

* Starcode:<ref>{{cite web|url=https://github.com/gui11aume/starcode|title=Starcode repository|date=2018-10-11}}</ref> a fast sequence clustering algorithm based on exact all-pairs search.<ref>{{cite journal

|title=Starcode: sequence clustering based on all-pairs search

|author1=Zorita E |author2=Cuscó P |author3=Filion GJ. |journal=Bioinformatics

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| date=Aug 2015 |volume=16

|issue=157

|pages=157 |pmid=26243257

|doi=10.1186/s13059-015-0721-2 |pmc=4531804}}</ref>

* Linclust:<ref>{{cite journal

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|author1=Steinegger M. |author2=Söding J. |journal=Nature Communications

|date=June 2018 |volume=9

|issue=1 |pages=2542

|doi=10.1038/s41467-018-04964-5

|pmid= 29959318|pmc=6026198 }}</ref> first algorithm whose runtime scales linearly with input set size, very fast, part of [http://mmseqs.org/ MMseqs2] <ref>{{cite journal

|title=MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

|author1=Steinegger M. |author2=Söding J. |journal=Nature Biotechnology

|date=Oct 16, 2017 |volume=35

|issue= 11|pages=1026–1028

|doi=10.1038/nbt.3988

|pmid= 29035372}}</ref> software suite for fast, sensitive sequence searching and clustering of large sequence sets

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* Clusterer:<ref>{{cite web|url=http://bugaco.com/bioinf/clusterer/|title=Clusterer: extendable java application for sequence grouping and cluster analyses|work=bugaco.com}}</ref> extendable java application for sequence grouping and cluster analyses

* PATDB: a program for rapidly identifying perfect substrings

* nrdb:<ref>{{Cite web | url=https://web.archive.org/web/20080101032917/http://blast.wustl.edu/pub/nrdb/ | title=Index of /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

* Skipredudant EMBOSS tool<ref>{{cite web|url=http://bioweb2.pasteur.fr/docs/EMBOSS/skipredundant.html|title=EMBOSS: skipredundant|work=pasteur.fr}}</ref> to remove redundant sequences from a set

* CLUSS Algorithm<ref>{{cite webjournal|urltitle=httpsCLUSS Algorithm ://bmcbioinformatics Clustering non-alignable protein sequences|journal=Prospectus.biomedcentralusherbrooke.com/articles/ca|volume=8|pages=286|doi=10.1186/1471-2105-8-286|titlepmid=CLUSS17683581|pmc=1976428|year Algorithm= :2007|last1 Clustering= non-alignableKelil|first1 protein= sequencesAbdellali|worklast2=prospectus.usherbrooke.caWang|first2=Shengrui|last3=Brzezinski|first3=Ryszard|last4=Fleury|first4=Alain}}</ref> to identify groups of structurally, functionally, or evolutionarily related hard-to-align protein sequences. CLUSS webserver <ref name="prospectus.usherbrooke.ca">{{Cite web | url=http://prospectus.usherbrooke.ca/CLUSS/ | title=CLUSS Home Page}}</ref>

* CLUSS2 Algorithm<ref>{{cite webjournal|url=https://www.inderscienceonline.com/doi/abs/10.1504/IJCBDD.2008.02019|title=CLUSS2 : Alignment-independent algorithm for clustering protein families with multiple biological functions|workissue=www2|pages=122–140|journal=International Journal of Computational Biology and Drug Design|volume=1|doi=10.inderscienceonline1504/IJCBDD.com2008.02019|date=January 2008|last1=Kelil|first1=Abdellali|last2=Wang|first2=Shengrui|last3=Brzezinski|first3=Ryszard|doi-broken-date=2018-11-28}}</ref> for clustering families of hard-to-align protein sequences with multiple biological functions. CLUSS2 webserver <ref name="prospectus.usherbrooke.ca"/>

<!-- Lets try the above (although both are wobbly) -->

<!-- * [http://bio.cc/RSDB RSDB] broken link -->

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| date=Jun 1998 |volume=14

|issue=5

|pages=423–9.

|title=Removing near-neighbour redundancy from large protein sequence collections.

|author=Holm L1, Sander C.

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|date= Nov 2016 |volume=45

|issue=D1 |pages= D170–D176

|doi= 10.1093/nar/gkw1081|pmid=27899574 |pmc=5614098 }}</ref>

* 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