title: BiDiBlast: comparative genomics pipeline for the PC.
abstract: Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http://moodle.fct.unl.pt/course/view.php?id=2079 or https://sourceforge.net/projects/bidiblast/ under the GNU GPL license.
authors.affiliation: Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, Caparica, Portugal. jmfa@fct.unl.pt
authors.forename: João M G C F
authors.initials: JM
authors.lastname: de Almeida
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D008838:Microcomputers; D011381:Programming Languages; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface