CisML: an XML-based format for sequence motif detection software

被引：6

作者：

Haverty, PM

Weng, ZP ^{[1
]}

机构：

[1] Boston Univ, Bioinformat Program, Boston, MA 02215 USA

[2] Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

来源：

BIOINFORMATICS | 2004年 / 20卷 / 11期

关键词：

D O I：

10.1093/bioinformatics/bth162

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

CisML is an XML-based format for sequence motif detection software. This proposed standard is applicable to many types of sequence motif detection programs. It is intended to facilitate the integration of data and the comparison of results from different software packages, and to simplify the development of downstream tools. XSL stylesheets are provided for easy generation of text, html and graphical reports from CisML-formatted data.

引用

页码：1815 / 1817

页数：3

共 10 条

[1] XML, bioinformatics and data integration
Achard, F
Vaysseix, G
Barillot, E
[J]. BIOINFORMATICS, 2001, 17 (02) : 115 - 125
[2] The biopolymer markup language
Fenyö, D
[J]. BIOINFORMATICS, 1999, 15 (04) : 339 - 340
[3] Cluster-Buster: finding dense clusters of motifs in DNA sequences
Frith, MC
Li, MC
Weng, ZP
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (13) : 3666 - 3668
[4] CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
Kurata, H
Matoba, N
Shimizu, N
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (14) : 4071 - 4084
[5] Mulder NJ, 2002, GENOME BIOL, V3
[6] MURRAYRUST P, 1995, ABSTR PAP AM CHEM S, V210, P40
[7] MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data
Quandt, K
Frech, K
Karas, H
Wingender, E
Werner, T
[J]. NUCLEIC ACIDS RESEARCH, 1995, 23 (23) : 4878 - 4884
[8] EMBOSS: The European molecular biology open software suite
Rice, P
Longden, I
Bleasby, A
[J]. TRENDS IN GENETICS, 2000, 16 (06) : 276 - 277
[9] Spellman PT, 2002, GENOME BIOL, V3
[10] DNA binding sites: representation and discovery
Stormo, GD
[J]. BIOINFORMATICS, 2000, 16 (01) : 16 - 23

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