SANSparallel : interactive homology search against Uniprot

Show full item record



Somervuo , P & Holm , L 2015 , ' SANSparallel : interactive homology search against Uniprot ' , Nucleic Acids Research , vol. 43 , no. W1 , pp. W24-W29 .

Title: SANSparallel : interactive homology search against Uniprot
Author: Somervuo, Panu; Holm, Liisa
Contributor organization: Biosciences
Institute of Biotechnology
Centre of Excellence in Metapopulation Research
Ecology and Evolutionary Biology
Computational genomics
Date: 2015-07-01
Language: eng
Number of pages: 6
Belongs to series: Nucleic Acids Research
ISSN: 0305-1048
Abstract: Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest.
1182 Biochemistry, cell and molecular biology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

Files in this item

Total number of downloads: Loading...

Files Size Format View
SANSparallel_in ... search_against_Uniprot.pdf 1.653Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record