AUTHOR=Zhang Xi , Hu Yining , Smith David Roy 

TITLE=HSDFinder: A BLAST-Based Strategy for Identifying Highly Similar Duplicated Genes in Eukaryotic Genomes

JOURNAL=Frontiers in Bioinformatics

VOLUME=1

YEAR=2021

URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2021.803176

DOI=10.3389/fbinf.2021.803176

ISSN=2673-7647

ABSTRACT=<p>Gene duplication is an important evolutionary mechanism capable of providing new genetic material for adaptive and nonadaptive evolution. However, bioinformatics tools for identifying duplicate genes are often limited to the detection of paralogs in multiple species or to specific types of gene duplicates, such as retrocopies. Here, we present a user-friendly, BLAST-based web tool, called HSDFinder, which can identify, annotate, categorize, and visualize highly similar duplicate genes (HSDs) in eukaryotic nuclear genomes. HSDFinder includes an online heatmap plotting option, allowing users to compare HSDs among different species and visualize the results in different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional categories. The external software requirements are BLAST, InterProScan, and KEGG. The utility of HSDFinder was tested on various model eukaryotic species, including <italic>Chlamydomonas reinhardtii</italic>, <italic>Arabidopsis thaliana</italic>, <italic>Oryza sativa</italic>, and <italic>Zea mays</italic> as well as the psychrophilic green alga <italic>Chlamydomonas</italic> sp. UWO241, and was proven to be a practical and accurate tool for gene duplication analyses. The web tool is free to use at <ext-link ext-link-type="uri" xlink:href="http://hsdfinder.com" xmlns:xlink="http://www.w3.org/1999/xlink">http://hsdfinder.com</ext-link>. Documentation and tutorials can be found via the GitHub: <ext-link ext-link-type="uri" xlink:href="https://github.com/zx0223winner/HSDFinder" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/zx0223winner/HSDFinder</ext-link>.</p>