ArticleBioinformatics (Oxford, England)2012
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs.Frontiers in bioinformatics · 2023Article
- Osmoprotectants play a major role in theFrontiers in plant science · 2023Article
- Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data ofBiology · 2022Article
- Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment.Journal of integrative bioinformatics · 2020Article
- TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases.BMC bioinformatics · 2018Article
- SANSparallel: interactive homology search against Uniprot.Nucleic acids research · 2015Article
- The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.Nature communications · 2014Article
- Lambda: the local aligner for massive biological data.Bioinformatics (Oxford, England) · 2014Article
- A fast Peptide Match service for UniProt Knowledgebase.Bioinformatics (Oxford, England) · 2013Article
- Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193.PLoS pathogens · 2012Article
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2 authors.
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Abstract
motivationThe genomic era in molecular biology has brought on a rapidly widening gap between the amount of sequence data and first-hand experimental characterization of proteins. Fortunately, the theory of evolution provides a simple solution: functional and structural information can be transferred between homologous proteins. Sequence similarity searching followed by k-nearest neighbor classification is the most widely used tool to predict the function or structure of anonymous gene products that come out of genome sequencing projects.
resultsWe present a novel word filter, suffix array neighborhood search (SANS), to identify protein sequence similarities in the range of 50-100% identity with sensitivity comparable to BLAST and 10 times the speed of USEARCH. In contrast to these previous approaches, the complexity of the search is proportional only to the length of the query sequence and independent of database size, enabling fast searching and functional annotation into the future despite rapidly expanding databases. AVAILABILITY AND IMPLEMENTATION: The software is freely available to non-commercial users from our website http://ekhidna.biocenter.helsinki.fi/downloads/sans. CONTACT: liisa.holm@helsinki.fi.
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