BlastDigester

Welcome to BlastDigester! Use Blast to identify a homologous region for your gene or region of interest within a database of e.g. ESTs or partial genomic sequence from another variety/pathovar/cultivar. BlastDigester will then take the Blast output, and identify the SNPs that are snip-SNPs, i.e. those that create a restriction site in one variety's DNA but not in the other's. The BlastDigester output links to the Primer3 program so that primers surrounding the snip-SNP of interest can be generated by a single mouse click. The resultant primers can then be tested as CAPS (Cleaved Amplified Polymorphic Sequence) markers, also known at PCR-RFLP markers. The citation for BlastDigester is Ilic K, Berleth T, Provart NJ, 2004. BlastDigester - a web-based program for efficient CAPS marker design. Trends in Genetics 20(7):280-283. Supplemental information for the primers presented in the TiG paper is available here. See Konieczny and Ausubel, 1993. Plant J. 4:403-10 for more information on CAPS markers. Parsing bug for newer Blast2Seq and Blast outputs from NCBI (up to Blast v.2.2.15) now fixed, so you may use the Blast2Seq option as before [2 Jan 2007]. Blast outputs in text format from sources other than NBCI must likely be tweaked to conform to the 'standard' Blast format - the syntax at the top of the output is especially important. Contact Nicholas Provart for help.

Based on diverse Bioperl modules. Runs locally on the Bio-Analytic Resource. Browser requirements: works best with Internet Explorer 5.5 or higher, but will also work with Netscape 6.0 or higher.
Show only differential cutters. If you check this, then only the differential cutters will be shown in the overview table.
Size of exclusion zone: bp. If the same cutsite is within this number of basepairs of a differential cutter then it will be flagged gray. Differential cutters that pass this criterion are otherwise coloured red or teal.
Select the Primer3 design parameters. These will be used to generate a dynamic link to the Primer3 program at the Whitehead Institute.

Primer Size Min: Opt: Max:

Primer Tm Min: Opt: Max:

Primer GC% Min: Opt: Max:

Product Size Tip
Simply browse to your BLAST output in plain text format below. Download an example BLAST output here (use right mouse button and save as...). Or paste a BLAST output into the box below. Note that the entire output must be submitted for BlastDigester to work. In the case of NCBI Blast2seq output, do Ctrl-A (select all) followed by Ctrl-C (copy), and paste the clipboard contents into the box below.
Then click Submit ...results may be explored in the browser. Click on a diffential cutter identified in red or teal in the alignment to have a primer pair, e.g. for CAPS markers, designed for you by Primer3 at the Whitehead Institute.

Upload a BLAST file :
Type of Output: Regular Blast, Blast2seq

Or paste BLAST output here (must be entire output!):