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1、BMCBioinformaticsBioMedCentralSoftwareOpenAccessBLAST+:architectureandapplicationsChristiamCamacho,GeorgeCoulouris,VahramAvagyan,NingMa,JasonPapadopoulos,KevinBealerandThomasLMadden*Address:NationalCenterforBiotechnologyInformation,NationalLibraryofMedicine,NationalInstitutesofHealth,Buildin
2、g38A,8600RockvillePike,Bethesda,MD20894,USAEmail:ChristiamCamacho-camacho@ncbi.nlm.nih.gov;GeorgeCoulouris-coulouri@ncbi.nlm.nih.gov;VahramAvagyan-avagyanv@ncbi.nlm.nih.gov;NingMa-maning@ncbi.nlm.nih.gov;JasonPapadopoulos-jasonp@boo.net;KevinBealer-kevinbealer@gmail.com;ThomasLMadden*-madden
3、@ncbi.nlm.nih.gov*CorrespondingauthorPublished:15December2009Received:28July2009Accepted:15December2009BMCBioinformatics2009,10:421doi:10.1186/1471-2105-10-421Thisarticleisavailablefrom:http://www.biomedcentral.com/1471-2105/10/421©2009Camachoetal;licenseeBioMedCentralLtd.ThisisanOpenAccessa
4、rticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(http://creativecommons.org/licenses/by/2.0),whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited.AbstractBackground:Sequencesimilaritysearchingisaveryimportantbioinforma
5、ticstask.WhileBasicLocalAlignmentSearchTool(BLAST)outperformsexactmethodsthroughitsuseofheuristics,thespeedofthecurrentBLASTsoftwareissuboptimalforverylongqueriesordatabasesequences.Therearealsosomeshortcomingsintheuser-interfaceofthecurrentcommand-lineapplications.Results:Wedescribefeatures
6、andimprovementsofrewrittenBLASTsoftwareandintroducenewcommand-lineapplications.Longquerysequencesarebrokenintochunksforprocessing,insomecasesleadingtodramaticallyshorterruntimes.Forlongdatabasesequences,itispossibletoretrieveonlytherelevantpartsofthesequence,reducingCPUtimeandmemoryusagefors
7、earchesofshortqueriesagainstdatabasesofcontigsorchromosomes.TheprogramcannowretrievemaskinginformationfordatabasesequencesfromtheBLASTdatabases.Anewmodularsoftwarelibrarycannowaccesssubjectsequencedatafromarbitrarydatasources.Weintroduceseveralnewf
