Batch fetch SNPs with flanking sequence

SNPSequer [snip 'si-kwer]

Batch query of SNPs -- obtain flanking sequences of sufficient length for SNP genotyping primer design

1. Please supply a list of SNPs rs IDs of dbSNP (must be prefixed with "rs", such as rs125, one ID per line) or a list of SNPs with flanking sequence in specified format : (Temporarily, if you use rs ID as input, only less than 20 SNPs could be processed in each batch due to restriction from BLAT at Genome Browser. SNPSequer is under renovation to remove this restriction. )

or upload a data file with this information

supplied data above is (Be sure to select the right one)

2. Desired flanking sequence length: bp at each side

3. Use to map SNPs and extract flanking sequences

4. Optional outputs:

    Data file with uniformed bp flanking sequences
    Data file for ABI TaqMan assay-by-design (ABI File Builder's input)
    "Marker data" file for Gene Manager (Internal DB, if this is selected, the flanking sequence will be uniformed to 50 bp, overwriting the option above. )

5. Please specify the email address where the results can be delivered:

Email address

6. Output desired in gzip compressed format?

Your email box accepts message size limit of per message

If your input data file is from a Mac machine, please be sure to check this box

NOTE:

Input (one of the following):

rs prefixed IDs from dbSNP
SNPs in DNannotator SNPs format

SNPSequer outputs data files of:

General FASTA format, suitable for most other softwares, including BLAST etc., named as "_SNP.fas".
DNannotator SNPs Input format, for DNannotator functions (such as for SNPs mapping), named as "_DNinput.txt"
Input data for some primer design tools (including Pyrosequencing, SNP Cutter etc.), named as "_typer.fas".
Reference information for SNPs with potential problems, named as "_mesg.txt".
ABI TaqMan Assay-by-design FileBuilder's input data, named as ".abd.txt".

Three different SNP mapping modes:

Fast Mode: use BLAT (with filter on) to map SNPs.
Medium Mode: use BLAT (with filter off) to map SNPs
Slow Mode: use BLAST to map SNPs.