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ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences
The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the wa...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8710255/ https://www.ncbi.nlm.nih.gov/pubmed/35036172 http://dx.doi.org/10.7717/peerj.12707 |
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author | Ejigu, Girum Fitihamlak Yi, Gangman Kim, Jong Im Jung, Jaehee |
author_facet | Ejigu, Girum Fitihamlak Yi, Gangman Kim, Jong Im Jung, Jaehee |
author_sort | Ejigu, Girum Fitihamlak |
collection | PubMed |
description | The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the way up to the whole-genome level. Homology-based approaches based on related reference sequences are usually the preferred option for gene and transcript prediction in newly sequenced genomes, resulting in the popularity of a variety of BLAST and BLAST-based tools. For organelle genomes, a single-reference–based gene finding tool that uses grouping parameters for BLAST results has been implemented in the Genome Search Plotter (GSP). However, this tool does not accept multiple and user-customized reference sequences required for a broad homology search. Here, we present multiple Reference–based Gene Search and Plot (ReGSP), a simple and convenient web tool that accepts multiple reference sequences for homology-based gene search. The tool incorporates cPlot, a novel dot plot tool, for illustrating nucleotide sequence similarity between the query and the reference sequences. ReGSP has an easy-to-use web interface and is freely accessible at https://ds.mju.ac.kr/regsp. |
format | Online Article Text |
id | pubmed-8710255 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-87102552022-01-14 ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences Ejigu, Girum Fitihamlak Yi, Gangman Kim, Jong Im Jung, Jaehee PeerJ Bioinformatics The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the way up to the whole-genome level. Homology-based approaches based on related reference sequences are usually the preferred option for gene and transcript prediction in newly sequenced genomes, resulting in the popularity of a variety of BLAST and BLAST-based tools. For organelle genomes, a single-reference–based gene finding tool that uses grouping parameters for BLAST results has been implemented in the Genome Search Plotter (GSP). However, this tool does not accept multiple and user-customized reference sequences required for a broad homology search. Here, we present multiple Reference–based Gene Search and Plot (ReGSP), a simple and convenient web tool that accepts multiple reference sequences for homology-based gene search. The tool incorporates cPlot, a novel dot plot tool, for illustrating nucleotide sequence similarity between the query and the reference sequences. ReGSP has an easy-to-use web interface and is freely accessible at https://ds.mju.ac.kr/regsp. PeerJ Inc. 2021-12-23 /pmc/articles/PMC8710255/ /pubmed/35036172 http://dx.doi.org/10.7717/peerj.12707 Text en ©2021 Ejigu et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Bioinformatics Ejigu, Girum Fitihamlak Yi, Gangman Kim, Jong Im Jung, Jaehee ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences |
title | ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences |
title_full | ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences |
title_fullStr | ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences |
title_full_unstemmed | ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences |
title_short | ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences |
title_sort | regsp: a visualized application for homology-based gene searching and plotting using multiple reference sequences |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8710255/ https://www.ncbi.nlm.nih.gov/pubmed/35036172 http://dx.doi.org/10.7717/peerj.12707 |
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