University of Helsinki

SANSparallel: Interactive homology search against Uniprot

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This server takes FASTA formatted sequences as input and returns similar sequences from the selected database. All results are returned immediately.

SANSparallel [1] is an MPI implementation of a suffix array neighborhood search client-server. The original SANS method [2] was improved, re-implemented as a client-server, and parallelized. The server can be accessed in a web browser or programmatically.

Web outputs are presented as tables, BLAST-like pairwise alignments, or stacked alignments which can be viewed in Jalview or as sequence logos. Programmatic access enables the building of bioinformatic pipelines, for example, for protein function prediction.

The method is extremely fast and as sensitive as BLAST above 50 % sequence identity. The performance of SANSparallel was comparable to DIAMOND, LAMBDA and LAST in our benchmarks [1].

References

  1. Somervuo P, Holm L (2015) SANSparallel: Interactive homology search against Uniprot. Nucl. Acids Res. 43:W24-W29. PDF
  2. Koskinen P, Holm L (2012) SANS: High-throughput retrieval of protein sequences allowing 50 % mismatches. Bioinformatics 28, i438-i443