FMiR: A Curated Resource of Mitochondrial DNA Information for Fish

PloS One
Naresh Sahebrao NagpureUttam Kumar Sarkar

Abstract

Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, f...Continue Reading

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Citations

Mar 17, 2016·Database : the Journal of Biological Databases and Curation·Naresh Sahebrao NagpureS Murali
Jul 29, 2017·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Zhong-Duo WangChu-Wu Liu
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Apr 20, 2018·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Boni Amin LaskarKailash Chandra
Feb 17, 2017·Scientific Reports·Iliyas RashidBasdeo Kushwaha
Jul 15, 2019·Mitochondrial DNA. Part B, Resources·Shantanu KunduVikas Kumar
Jan 7, 2019·Genomics·Ajey Kumar PathakAnil Rai

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Methods Mentioned

BETA
PCR
genotyping

Software Mentioned

SubParse
MySQL PHP Perl
FMiR workbench
MitoZoa
Linux
MISA
Blastn
MitoFish
dloopdb
Blastx

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