StellaBase: Nematostella vectensis Genomics and Transcriptomics Database

Welcome to the StellaSNP search

As of 02/01/07, ~16,000 Nematostella EST transcsripts have bene published in the NCBI dbEST database. We have used TIGR's clustering software (tgicl) and Dave Edward's AutoSNP SNP identification software to assmeble these EST's and identify SNPs. Our search criteria are permissive and allow for the identification of any potential SNPs, including polymorphisms identified between as few as 2 sequences. Use this search engine to identify potential SNPs which match your permissiveness thresholds.
Note that you can also browse all contigs with SNPs and blast the EST contig database.

A tool to download individual assembled EST contigs is also available.

1. Please Choose: Help

Pfam accession   OR  Protein Family Name   OR StellaBase ID #   

2. Please Choose an e-value threshold: (Note: This e-value threshold will limit the number of EST contigs which match a specific PFAM motif) Help

3. Minimum Redundancy = the number of polymorphic bases at a base position. For example, assume that there are 10 distinct ESTs for GeneX. Assume that either a C, T, or G may be found at position n of GeneX. If C is found at position x in 8 ESTs, and T and G are each found at position x in 1 EST then the Miminum Redunancy is 3.

4. Select only those cDNAs which have at least this number of SNPs which match my redundancy threshold.

5. Submit Your Query:

Please Note: This search may take several seconds or minutes, particularly if you search using a PFAM Accession #.
Nematostella vectensis Genomics & Transcriptomics Database
Created by: Tristan Lubinski, Brian Granger, Jim Sullivan,
Joe Ryan, Adam Reitzel, Rachel Schweiker, and Sarah McAnulty
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