dbVAST stands for Database of Variations Associated with Shrimp Transcripts. It is a comprehensive database that houses information about non-synonymous SNP (Single Nucleotide Polymorphism) data and its significance (pathways, effects, protein stability etc.) in two shrimp species: Penaeus vannamei and Penaeus indicus.

You can access the dbVAST @ [website URL].

Currently, dbVAST provides support to search for SNPs in the coding sequence of two species of shrimp: Penaeus vannamei and Penaeus indicus.

For each SNP entry in dbVAST, you will find the following information:

• SNP ID: A unique identifier for the SNP.
• Nonsynonymous/Synonymous SNP: Type of SNP variation
• Pathways: KEGG pathway information for the SNP-harbouring transcript providing insights into potential functional implications.
• Functional impact of SNP: SIFT score (SNP is deleterious or tolerated), PANTHER evaluation (potential damaging effects of the SNP), I-Mutant evaluation (stability of resulting protein).

Absolutely. dbVAST provides flexible search options that allow you to search for SNPs based on species and specific criteria of interest. Here is how you can search for SNPs:

• Visit the dbVAST website at [website URL].
• On the homepage, you will find options to select the species. Choose either Penaeus vannamei or Penaeus indicus, depending on your preference.
• Once you have selected the species, you can proceed with the following two search approaches:

  Searching by Sequence:

  • Copy the sequence of interest (either nucleotide or protein) in fasta format.
  • Paste the Fasta sequence into the designated search field on the website.
  • Click on the "Submit" or "Search" button to initiate the search.
  • dbVAST will process the sequence and display the SNP details associated with the provided sequence.

  Searching by Protein Name:

  • Type the specific protein name of interest into the designated search field on the website.
  • Click on the "Submit" or "Search" button to initiate the search.
  • dbVAST will process the protein name and display the SNP details associated with that protein.

The search results will provide you with the relevant SNP details, including information about the SNP ID, nonsynonymous variations, significance (deleterious or tolerated), stability, damaging effects, benign effects, and associated pathways.

Currently, the database is curated by a team of researchers, but if you have relevant SNP data or additional information that could enhance the database, you can contact us using the provided contact details on the website. We welcome collaborations and contributions to further enrich the dbVAST resource.

If you encounter any issues while using the dbVAST website or have feedback or suggestions for improvement, please feel free to contact us using the provided contact information on the website. We appreciate your input and will strive to address any problems or concerns promptly.

Yes. The source code of dbVAST is freely available at Github, vinayciba/dbVAST

Yes. The dbVAST would be expanded with SNP data of other shrimp species as and when appropriate datasets become available in public repositories.

Yes. The users can download the table of SNP statistics that contains the SNP base positions, the two alleles at the SNP position and the quality metrics indicating the accuracy of the SNP position.

Yes, at dbVAST, you can access the functional significance of the SNPs with the result of various tools, including SIFT, PANTHER, and I-Mutant. This will provide valuable insights about the functional impact of the identified SNPs.

Certainly. At dbVAST, you have the option to retrieve SNPs associated with a specific protein by providing its name. This feature allows you to focus on SNPs within your protein of interest, facilitating targeted analysis and exploration.

At dbVAST, SNPs are selected for inclusion based on specific criteria to ensure data quality and reliability. The following criteria are used to determine whether a SNP is included in the database:

• Raw Read Depth: SNPs must have a raw read depth at the SNP site of ≥ 20.
• Read Support: Both the reference and alternate alleles of the SNP must be supported by at least 5 reads.
• Quality Score: The phred-scaled quality score for the assertion made in the alternate allele must be ≥ 100.