ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences

Author:

Ejigu Girum Fitihamlak1,Yi Gangman2,Kim Jong Im3,Jung Jaehee1

Affiliation:

1. Department of Information and Communication Engineering, Myongji University, Yongin-si, Gyeonggi-do, South Korea

2. Department of Multimedia Engineering, Dongguk University, Seoul, South Korea

3. Department of Biology, Chungnam National University, Daejeon, South Korea

Abstract

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.

Funder

the National Research Foundation of Korea (NRF) funded by the Ministry of Science

ICT and Future Planning

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Reference29 articles.

1. Basic local alignment search tool;Altschul;Journal of Molecular Biology,1990

2. Is it time to change the reference genome?;Ballouz;Genome Biology,2019

3. Prediction of complete gene structures in human genomic DNA;Burge;Journal of Molecular Biology,1997

4. UniProt: the universal protein knowledgebase in 2021;Consortium;Nucleic Acids Research,2021

5. Improved microbial gene identification with GLIMMER;Delcher;Nucleic Acids Research,1999

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