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Bioinformatics Advance Access first published online on May 30, 2007
This version published online on June 27, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm269
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

StrBioLib: a Java library for development of custom computational structural biology applications

John-Marc Chandonia *

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA

*To whom correspondence should be addressed. Dr. John-Marc Chandonia, E-mail: jmchandonia{at}lbl.gov


  Abstract

Summary: StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves nonlinear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the ASTRAL compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below.

Availability: StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/

Associate Editor: Dr. Alex Bateman

Received on March 21, 2007; revised on May 3, 2007; accepted on May 10, 2007

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