dbVAST: A web server for single nucleotide polymorphism variations in penaeid shrimp

Abstract Although farmed shrimp contribute to global food security and foreign exchange, the development of genomic resources such as single nucleotide polymorphisms for these shrimp is at slow pace. Public genomic resources like Genbank and Ensembl do not host polymorphism data for shrimp. Therefore, through analysis of the short RNA‐sequence reads generated on pooled‐individual samples, using the latest bioinformatics tools, this study documents data of single nucleotide polymorphisms in two shrimp species, Penaeus vannamei and Penaeus indicus , and presents these data in a searchable user‐friendly webtool, the dbVAST. The webtool also hosts the information about the possible effects that the variations could have on the functioning of the coded protein. This is the first open‐access SNP database of shrimp intended to benefit researchers and academicians by showcasing variations in shrimp transcripts.

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Publication Details

Journal
Invertebrate Biology
Published
2024-10-16
DOI
https://doi.org/10.1111/ivb.12445
Primary Topic
Crustacean biology and ecology
Type
article
Field-Weighted Citation Impact
0.00

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article

dbVAST: A web server for single nucleotide polymorphism variations in penaeid shrimp

Sudheesh K. Prabhudas, Ashok Kumar Jangam, Karthic Krishnan, Shashi Shekhar Mudagandur et al.
1 links
Invertebrate Biology
Crustacean biology and ecology
article

dbVAST: A web server for single nucleotide polymorphism variations in penaeid shrimp

Sudheesh K. Prabhudas, Ashok Kumar Jangam, Karthic Krishnan, Shashi Shekhar Mudagandur, Syama Dayal Jagabattula, Gangaraj Karyath Palliyath, Nimisha Kaikkolante, Vinaya Kumar Katneni, Vijayan K. Koyadan, R. Jayaraman, Dinesh Babu Selvababu
article en

Abstract

Abstract Although farmed shrimp contribute to global food security and foreign exchange, the development of genomic resources such as single nucleotide polymorphisms for these shrimp is at slow pace. Public genomic resources like Genbank and Ensembl do not host polymorphism data for shrimp. Therefore, through analysis of the short RNA‐sequence reads generated on pooled‐individual samples, using the latest bioinformatics tools, this study documents data of single nucleotide polymorphisms in two shrimp species, Penaeus vannamei and Penaeus indicus , and presents these data in a searchable user‐friendly webtool, the dbVAST. The webtool also hosts the information about the possible effects that the variations could have on the functioning of the coded protein. This is the first open‐access SNP database of shrimp intended to benefit researchers and academicians by showcasing variations in shrimp transcripts.

Invertebrate BiologyVol. 143(4)
Central Institute of Brackishwater Aquaculture (IN)
Department of Science and Technology, Ministry of Science and Technology, India, Indian Council of Agricultural Research
Zero hunger
Openalex Percentile: Top 82%
Crustacean biology and ecology
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