Abstract
In this article is presented and evaluated ABMS (Automatic BLAST for Massive Sequencing) an online bioinformatic free tool designed with the objective to automate and optimize the search process through local alignments for large unknown nucleotide or aminoacid sequence data against local known sequence databases (Swissprot, Uniprot, Refseq, among others). ABMS integrates the following processes: sequence entry management, proteome, genome and transcriptome database management, BLAST execution (blastp, blastx, blastn, tblastn) , and results management; these are presented to the biologist as an unified process, transparent with a friendly web interface. ABMS is built with the following modules: SM (Sequence manager), LBS (Local BLAST Server), SDBA (Sequence database administrator), RM (Results manager).Assessing ABMS with 2 data set (20/500 aminoacid sequences and 20/500 nucleotide) and compare its performance against NBCI’s BLAST server showed that: The strength of ABMS for massive sequence analysis and the of NBCI’s BLAST (both blastx and blastp) for data sets with more than 20 sequences. The advantages of ABMS against NBCI’s BLAST in terms of administration, data set storage, management, download and results feedback.
Work done in collaboration with High Performance Computational Center (CECAD) - Distrital University Francisco José de Caldas, Bogotá D.C., Colombia ( http://cecad.udistrital.edu.co ) and Genetics Institute - National University (IGUN ), Colombia, ( http://www.genetica.unal.edu.co ).
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Parra, N.E.V., Castillo, J.N.P., Quintero, C.A.R. (2014). Presentation and Evaluation of ABMS (Automatic Blast for Massive Sequencing). In: Castillo, L., Cristancho, M., Isaza, G., Pinzón, A., Rodríguez, J. (eds) Advances in Computational Biology. Advances in Intelligent Systems and Computing, vol 232. Springer, Cham. https://doi.org/10.1007/978-3-319-01568-2_29
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DOI: https://doi.org/10.1007/978-3-319-01568-2_29
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