Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduc...

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Autores principales: Tan, Joshua, Kuchibhatla, Durga, Sirota, Fernanda L., Sherman, Westley A., Gattermayer, Tobias, Kwoh, Chia Yee, Eisenhaber, Frank, Schneider, Georg, Maurer-Stroh, Sebastian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371831/
https://www.ncbi.nlm.nih.gov/pubmed/22531216
http://dx.doi.org/10.1093/bioinformatics/bts197
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author Tan, Joshua
Kuchibhatla, Durga
Sirota, Fernanda L.
Sherman, Westley A.
Gattermayer, Tobias
Kwoh, Chia Yee
Eisenhaber, Frank
Schneider, Georg
Maurer-Stroh, Sebastian
author_facet Tan, Joshua
Kuchibhatla, Durga
Sirota, Fernanda L.
Sherman, Westley A.
Gattermayer, Tobias
Kwoh, Chia Yee
Eisenhaber, Frank
Schneider, Georg
Maurer-Stroh, Sebastian
author_sort Tan, Joshua
collection PubMed
description Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. Availability and implementation: The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP. Contact: sebastianms@bii.a-star.edu.sg Supplementary information: Supplementary data are available at the Bioinformatics online.
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spelling pubmed-33718312012-06-11 Tachyon search speeds up retrieval of similar sequences by several orders of magnitude Tan, Joshua Kuchibhatla, Durga Sirota, Fernanda L. Sherman, Westley A. Gattermayer, Tobias Kwoh, Chia Yee Eisenhaber, Frank Schneider, Georg Maurer-Stroh, Sebastian Bioinformatics Applications Note Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. Availability and implementation: The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP. Contact: sebastianms@bii.a-star.edu.sg Supplementary information: Supplementary data are available at the Bioinformatics online. Oxford University Press 2012-06-15 2012-04-23 /pmc/articles/PMC3371831/ /pubmed/22531216 http://dx.doi.org/10.1093/bioinformatics/bts197 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Tan, Joshua
Kuchibhatla, Durga
Sirota, Fernanda L.
Sherman, Westley A.
Gattermayer, Tobias
Kwoh, Chia Yee
Eisenhaber, Frank
Schneider, Georg
Maurer-Stroh, Sebastian
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
title Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
title_full Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
title_fullStr Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
title_full_unstemmed Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
title_short Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
title_sort tachyon search speeds up retrieval of similar sequences by several orders of magnitude
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371831/
https://www.ncbi.nlm.nih.gov/pubmed/22531216
http://dx.doi.org/10.1093/bioinformatics/bts197
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