GeCo++: a C++ library for genomic features computation and annotation in the presence of variants

• DOI: 10.1093/bioinformatics/btr123
• Publication Date: 2011-03-13T23:38:49Z
• Authors: Matteo Cereda; Manuela Sironi; Matteo Cavalleri; Uberto Pozzoli
• Keywords: Base Sequence; 0206 medical engineering; Programming Languages; Genomics; Sequence Analysis, DNA; 02 engineering and technology; Sequence Alignment; Algorithms; Software; Algorithms; Base Sequence; Gene Library; Genomics; Programming Languages; Sequence Alignment; Sequence Analysis, DNA; Software; Gene Library

Abstract Summary: We propose a C++ class library developed to the purpose of making the implementation of sequence analysis algorithms easier and faster when genomic annotations and variations need to be considered. The library provides a class hierarchy to seamlessly bind together annotations of genomic elements to sequences and to algorithm results; it allows to evaluate the effect of mutations/variations in terms of both element position shifts and of algorithm results, limiting recalculation to the minimum. Particular care has been posed to keep memory and time overhead into acceptable limits. Availability and Implementation: A complete tutorial as well as a detailed doxygen generated documentation and source code is freely available at http://bioinformatics.emedea.it/geco, under the GPL license. The library was written in standard ISO C++, and does not depend on external libraries. Contact: [e-mail]