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EASER: Ensembl Easy Sequence Retriever

The rapid advances in genome sequencing technologies have increased the pace at which biological sequence databases are becoming available to the broad scientific community. Thus, obtaining and preparing an appropriate sequence dataset is a crucial first step for all types of genomic analyses. Here,...

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Detalles Bibliográficos
Autores principales: Maldonado, Emanuel, Khan, Imran, Philip, Siby, Vasconcelos, Vítor, Antunes, Agostinho
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Libertas Academica 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855309/
https://www.ncbi.nlm.nih.gov/pubmed/24324324
http://dx.doi.org/10.4137/EBO.S11335
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author Maldonado, Emanuel
Khan, Imran
Philip, Siby
Vasconcelos, Vítor
Antunes, Agostinho
author_facet Maldonado, Emanuel
Khan, Imran
Philip, Siby
Vasconcelos, Vítor
Antunes, Agostinho
author_sort Maldonado, Emanuel
collection PubMed
description The rapid advances in genome sequencing technologies have increased the pace at which biological sequence databases are becoming available to the broad scientific community. Thus, obtaining and preparing an appropriate sequence dataset is a crucial first step for all types of genomic analyses. Here, we present a script that can widely facilitate the easy, fast, and effortless downloading and preparation of a proper biological sequence dataset for various genomics studies. This script retrieves Ensembl defined genomic features, associated with a given Ensembl identifier. Coding (CDS) and genomic sequences can be easily retrieved based on a selected relationship from a set of relationship types, either considering all available organisms or a user specified subset of organisms. The script is very user-friendly and by default starts with an interactive mode if no command-line options are specified.
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spelling pubmed-38553092013-12-09 EASER: Ensembl Easy Sequence Retriever Maldonado, Emanuel Khan, Imran Philip, Siby Vasconcelos, Vítor Antunes, Agostinho Evol Bioinform Online Technical Advance The rapid advances in genome sequencing technologies have increased the pace at which biological sequence databases are becoming available to the broad scientific community. Thus, obtaining and preparing an appropriate sequence dataset is a crucial first step for all types of genomic analyses. Here, we present a script that can widely facilitate the easy, fast, and effortless downloading and preparation of a proper biological sequence dataset for various genomics studies. This script retrieves Ensembl defined genomic features, associated with a given Ensembl identifier. Coding (CDS) and genomic sequences can be easily retrieved based on a selected relationship from a set of relationship types, either considering all available organisms or a user specified subset of organisms. The script is very user-friendly and by default starts with an interactive mode if no command-line options are specified. Libertas Academica 2013-11-24 /pmc/articles/PMC3855309/ /pubmed/24324324 http://dx.doi.org/10.4137/EBO.S11335 Text en © 2013 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License.
spellingShingle Technical Advance
Maldonado, Emanuel
Khan, Imran
Philip, Siby
Vasconcelos, Vítor
Antunes, Agostinho
EASER: Ensembl Easy Sequence Retriever
title EASER: Ensembl Easy Sequence Retriever
title_full EASER: Ensembl Easy Sequence Retriever
title_fullStr EASER: Ensembl Easy Sequence Retriever
title_full_unstemmed EASER: Ensembl Easy Sequence Retriever
title_short EASER: Ensembl Easy Sequence Retriever
title_sort easer: ensembl easy sequence retriever
topic Technical Advance
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855309/
https://www.ncbi.nlm.nih.gov/pubmed/24324324
http://dx.doi.org/10.4137/EBO.S11335
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