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WGCCRR: a web-based tool for genome-wide screening of convergent indels and substitutions of amino-acids

Dong, Zheng, Wang, Chen, Qu, Qingming·2024·Bioinformatics Advances
DOI 10.1093/bioadv/vbae070PMC PMC11132816
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Abstract

Summary: Genome-wide analyses of proteincoding gene sequences are being employed to examine the genetic basis of adaptive evolution in many organismal groups. Previous studies have revealed that convergent/parallel adaptive evolution may be caused by convergent/parallel amino acid changes. Similarly, detailed analysis of lineage-specific amino acid changes has shown correlations with certain lineage-specific traits. However, experimental validation remains the ultimate measure of causality. With the increasing availability of genomic data, a streamlined tool for such analyses would facilitate and expedite the screening of genetic loci that hold potential for adaptive evolution, while alleviating the bioinformatic burden for experimental biologists. In this study, we present a user-friendly web-based tool called WGCCRR (Whole Genome Comparative Coding Region Read) designed to screen both convergent/parallel and lineage-specific amino acid changes on a genome-wide scale. Our tool allows users to replicate previous analyses with just a few clicks, and the exported results are straightforward to interpret. In addition, we have also included amino acid indels that are usually neglected in previous work. Our website provides an efficient platform for screening candidate loci for downstream experimental tests. Availability and Implementation: The tool is available at: https://fishevo.xmu.edu.cn/.

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Metadata

Authors
Dong, Z., Wang, C., & Qu, Q.
Affiliations
State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University , Xià-Mén, Fú-Jiàn 361102, China
ORCID
Qu, Qingming
Venue
Bioinformatics Advances
Publisher
Oxford University Press (OUP)
Published
2024-01-01
Volume
4
Issue
1
ISSN
2635-0041
DOI
10.1093/bioadv/vbae070
PMC
PMC11132816
Cited by
2
References
2
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor, 144 d)
Funders
  • Xiamen University
  • National Natural Science Foundation of China (42272013)

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