AlignBucket

The tool AlignBucket provides an algorithm that optimizes the partition of a large volume of sequences into sets, where sequence length values are constrained depending on a bounded minimal and expected alignment coverage. This helps to reduce the time of sequence comparison by grouping protein sequences according to their length and then computing the all-against-all sequence alignments among sequences that fall in a selected length range. The tool shows a 5-fold speed-up in real-world cases.

Topic

Sequence analysis;Protein sites, features and motifs

Detail

  • Operation: Splitting;Sequence alignment

  • Software interface: Command-line user interface

  • Language: Shell;C++;Python

  • License: GNU Public License version 2

  • Cost: Free

  • Version name: -

  • Credit: COST BMBS Action TD1101 and Action BM1405, PON projects PON01_02249, PAN Lab Italian Ministry of University and Research, FARB-UNIBO 2012.

  • Input: FASTA

  • Output: -

  • Contact: Giuseppe Profiti giuseppe.profiti2@unibo.it

  • Collection: -

  • Maturity: -

Publications

Download and documentation

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