BioJava']Java: an open-source framework for bioinformatics in 2012

被引：128

作者：

Prlic, Andreas ^{[1
]}

Yates, Andrew ^{[2
]}

Bliven, Spencer E. ^{[3
]}

Rose, Peter W. ^{[1
]}

Jacobsen, Julius ^{[2
]}

Troshin, Peter V. ^{[4
]}

Chapman, Mark ^{[5
]}

Gao, Jianjiong ^{[6
]}

Koh, Chuan Hock ^{[7
]}

Foisy, Sylvain ^{[8
]}

Holland, Richard ^{[9
]}

Rimsa, Gediminas ^{[10
]}

Heuer, Michael L. ^{[11
]}

Brandstaetter-Mueller, H. ^{[12
]}

Bourne, Philip E. ^{[13
]}

Willis, Scooter ^{[14
]}

机构：

[1] Univ Calif San Diego, San Diego Supercomp Ctr, La Jolla, CA 92093 USA

[2] European Bioinformat Inst, Cambridge CB10 1SD, England

[3] Univ Calif San Diego, Bioinformat Program, La Jolla, CA 92093 USA

[4] Univ Dundee, Coll Life Sci, Dundee DD1 5EH, Scotland

[5] Univ Wisconsin Madison, Dept Comp Sci, Madison, WI 53706 USA

[6] Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10065 USA

[7] NUS Grad Sch Integrat Sci & Engn, Singapore 117597, Singapore

[8] Montreal Heart Inst, Montreal, PQ H1T 1C8, Canada

[9] Eagle Genom Ltd, Cambridge CB22 3AT, England

[10] Vilnius Univ, Fac Math & Informat, LT-03225 Vilnius, Lithuania

[11] Harbinger Partners Inc, St Paul, MN 55127 USA

[12] Univ Appl Sci Upper Austria, A-4232 Hagenberg, Austria

[13] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA

[14] Scripps Florida, Genom Core, Jupiter, FL 33458 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 20期

基金：

美国国家科学基金会;

关键词：

PROTEIN DATA-BANK; MOLECULAR-BIOLOGY; ANNOTATION; SOFTWARE; SEQUENCE; ALIGNMENTS; RESOURCE; TOOLKIT; FILE;

D O I：

10.1093/bioinformatics/bts494

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.

引用

页码：2693 / 2695

页数：3

共 30 条

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