BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases

Konstantinos Bimpikis; Aidan Budd; Rune Linding; Toby J Gibson

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases

Konstantinos Bimpikis, Aidan Budd, Rune Linding, Toby J Gibson

Research output: Contribution to journal › Journal article › Research › peer-review

5 Citations (Scopus)

Abstract

SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available. However, with the increasingly large datasets available it is now quite common that a user is interested in some subset of homologous sequences but has no efficient way to restrict retrieval to that set. By allowing the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword.

Original language	English
Journal	Nucleic Acids Research
Volume	31
Issue number	13
Pages (from-to)	3792-4
Number of pages	3
ISSN	0305-1048
Publication status	Published - 1 Jul 2003
Externally published	Yes

Keywords

Animals
Databases, Protein
Humans
Internet
Sequence Homology, Amino Acid
Software
User-Computer Interface

Cite this

@article{bec3ad756a1f46babd4ac406062cb177,

title = "BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases",

abstract = "SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available. However, with the increasingly large datasets available it is now quite common that a user is interested in some subset of homologous sequences but has no efficient way to restrict retrieval to that set. By allowing the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword.",

keywords = "Animals, Databases, Protein, Humans, Internet, Sequence Homology, Amino Acid, Software, User-Computer Interface",

author = "Konstantinos Bimpikis and Aidan Budd and Rune Linding and Gibson, {Toby J}",

year = "2003",

month = jul,

day = "1",

language = "English",

volume = "31",

pages = "3792--4",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "13",

}

TY - JOUR

T1 - BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases

AU - Bimpikis, Konstantinos

AU - Budd, Aidan

AU - Linding, Rune

AU - Gibson, Toby J

PY - 2003/7/1

Y1 - 2003/7/1

N2 - SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available. However, with the increasingly large datasets available it is now quite common that a user is interested in some subset of homologous sequences but has no efficient way to restrict retrieval to that set. By allowing the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword.

AB - SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available. However, with the increasingly large datasets available it is now quite common that a user is interested in some subset of homologous sequences but has no efficient way to restrict retrieval to that set. By allowing the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword.

KW - Animals

KW - Databases, Protein

KW - Humans

KW - Internet

KW - Sequence Homology, Amino Acid

KW - Software

KW - User-Computer Interface

M3 - Journal article

C2 - 12824420

SN - 0305-1048

VL - 31

SP - 3792

EP - 3794

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 13

ER -