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GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts

GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly...

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Detalles Bibliográficos
Autores principales: Naito, Yuki, Bono, Hidemasa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394333/
https://www.ncbi.nlm.nih.gov/pubmed/22641850
http://dx.doi.org/10.1093/nar/gks448
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author Naito, Yuki
Bono, Hidemasa
author_facet Naito, Yuki
Bono, Hidemasa
author_sort Naito, Yuki
collection PubMed
description GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant RefSeq transcripts. A typical search takes just a few seconds, which dramatically enhances the usability of routine searching. In particular, GGRNA can search sequences as short as 10 nt or 4 amino acids, which cannot be handled easily by popular sequence analysis tools. Nucleotide sequences can be searched allowing up to three mismatches, or the query sequences may contain degenerate nucleotide codes (e.g. N, R, Y, S). Furthermore, Gene Ontology annotations, Enzyme Commission numbers and probe sequences of catalog microarrays are also incorporated into GGRNA, which may help users to conduct searches by various types of keywords. GGRNA web server will provide a simple and powerful interface for finding genes and transcripts for a wide range of users. All services at GGRNA are provided free of charge to all users.
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spelling pubmed-33943332012-07-30 GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts Naito, Yuki Bono, Hidemasa Nucleic Acids Res Articles GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant RefSeq transcripts. A typical search takes just a few seconds, which dramatically enhances the usability of routine searching. In particular, GGRNA can search sequences as short as 10 nt or 4 amino acids, which cannot be handled easily by popular sequence analysis tools. Nucleotide sequences can be searched allowing up to three mismatches, or the query sequences may contain degenerate nucleotide codes (e.g. N, R, Y, S). Furthermore, Gene Ontology annotations, Enzyme Commission numbers and probe sequences of catalog microarrays are also incorporated into GGRNA, which may help users to conduct searches by various types of keywords. GGRNA web server will provide a simple and powerful interface for finding genes and transcripts for a wide range of users. All services at GGRNA are provided free of charge to all users. Oxford University Press 2012-07 2012-05-28 /pmc/articles/PMC3394333/ /pubmed/22641850 http://dx.doi.org/10.1093/nar/gks448 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 Articles
Naito, Yuki
Bono, Hidemasa
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts
title GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts
title_full GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts
title_fullStr GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts
title_full_unstemmed GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts
title_short GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts
title_sort ggrna: an ultrafast, transcript-oriented search engine for genes and transcripts
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394333/
https://www.ncbi.nlm.nih.gov/pubmed/22641850
http://dx.doi.org/10.1093/nar/gks448
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