AlignBucket | Datasets2Tools

General Information

Description	A tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints
Homepage	http://www.biocomp.unibo.it/~giuseppe/partitioning.html

Publications

Bioinformatics (2015)

AlignBucket: a tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints

Giuseppe Profiti; Piero Fariselli; Rita Casadio

Motivation: The next-generation sequencing era requires reliable, fast and efficient approaches for the accurate annotation of the ever-increasing number of biological sequences and their variations. Transfer of annotation upon similarity search is a standard approach. The procedure of all-against-all protein comparison is a preliminary step of different available methods that annotate sequences based on information already present in databases. Given the actual volume of sequences, methods are necessary to pre-process data to reduce the time of sequence comparison.

Results: We present an algorithm that optimizes the partition of a large volume of sequences (the whole database) into sets where sequence length values (in residues) are constrained depending on a bounded minimal and expected alignment coverage. The idea is to optimally group protein sequences according to their length, and then computing the all-against-all sequence alignments among sequences that fall in a selected length range. We describe a mathematically optimal solution and we show that our method leads to a 5-fold speed-up in real world cases.

Availability and implementation: The software is available for downloading at http://www.biocomp.unibo.it/∼giuseppe/partitioning.html.

Contact: giuseppe.profiti2@unibo.it

Supplementary information: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btv451

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