ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ

被引：15

作者：

del Val, C. ^{[1
,2
]}

Ernst, P. ^{[1
]}

Falkenhahn, M. ^{[1
]}

Fladerer, C. ^{[1
]}

Glatting, K. H. ^{[1
]}

Suhai, S. ^{[1
]}

Hotz-Wagenblatt, A. ^{[1
]}

机构：

[1] Deutsch Krebsforschungszentrum, Res Ctr, Div Mol Biophys, D-69120 Heidelberg, Germany

[2] Univ Granada, ETSII, Dept Comp Sci & Artificial Intelligence, E-18071 Granada, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

关键词：

D O I：

10.1093/nar/gkm364

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The wealth of transcript information that has been made publicly available in recent years has led to large pools of individual web sites offering access to bioinformatics software. However, finding out which services exist, what they can or cannot do, how to use them and how to feed results from one service to the next one in the right format can be very time and resource consuming, especially for non-experts. Automating this task, we present a suite of protein annotation pipelines (tasks) developed at the German Cancer Research Centre (DKFZ) oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep). The aim of these tasks is to perform an exhaustive structural and functional analysis employing a wide variety of methods in combination with the most updated public databases. The three servers are available for academic users at the HUSAR open server http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar/.

引用

页码：W444 / W450

页数：7

共 32 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, SF
Madden, TL
Schaffer, AA
Zhang, JH
Zhang, Z
Miller, W
Lipman, DJ
[J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (17) : 3389 - 3402
[2] BASIC LOCAL ALIGNMENT SEARCH TOOL
ALTSCHUL, SF
GISH, W
MILLER, W
MYERS, EW
LIPMAN, DJ
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
[3] ANDREEVA A, 2004, SCOP DATABASE 2004 R
[4] PRINTS and its automatic supplement, prePRINTS
Attwood, TK
Bradley, P
Flower, DR
Gaulton, A
Maudling, N
Mitchell, AL
Moulton, G
Nordle, A
Paine, K
Taylor, P
Uddin, A
Zygouri, C
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (01) : 400 - 402
[5] BANNASCH D, 2004, NUCL ACIDS RES, V32
[6] Bateman A, 2002, NUCLEIC ACIDS RES, V30, P276, DOI [10.1093/nar/gkr1065, 10.1093/nar/gkp985, 10.1093/nar/gkh121]
[7] The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
Boeckmann, B
Bairoch, A
Apweiler, R
Blatter, MC
Estreicher, A
Gasteiger, E
Martin, MJ
Michoud, K
O'Donovan, C
Phan, I
Pilbout, S
Schneider, M
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (01) : 365 - 370
[8] ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons
Corpet, F
Servant, F
Gouzy, J
Kahn, D
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 267 - 269
[9] TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter
Cserzo, M
Eisenhaber, F
Eisenhaber, B
Simon, I
[J]. BIOINFORMATICS, 2004, 20 (01) : 136 - 137
[10] Cuff JA, 2000, PROTEINS, V40, P502, DOI 10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO

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