Map SNPs to UCSC latest freeze

* entries are required

BLAT created by Jim Kent, 2002 is used

1. *Please copy & paste in the SNPs data in proper format:

or upload data file

2. Please select the chromosome the SNPs are mapping to:

   * Chromosome of latest version of UCSC freeze (be sure to select the correct one)

3. Adjustable parameters.

Use to map SNPs

Additional parameters for BLAT-based annotation:

Additional parameters for BLAST-based annotation:

For annotation,

@ Minimum size of match for valid hits  bp for full range of normal SNPs; bp for each ends of insertion/deletions, (If your SNP is with shorter flanking sequences, please decrease this number accordingly)

@ Minimum percentage of identities for valid hits

@ The maximum length difference between query SNP and matching fragment is bp

@

4. Choice of outputs:

    Show BLAST/BLAT annotation evidence of match identity percentage in Genbank annotation and features table

    Annotation Genbank format data or Genbank format features (gbheader)

        viewable in Vector NTI  or Artemis

    Feature table ready for database in tab-delimited format 

    Features failed to be annotated

    Duplicated features (possibly false positive due to homologs)

    Original BLAST/BLAT output

    Data for the "custom track" of Genome Browser
         Name the track as

    Annotation evidence (compact parsed BLAST/BLAT data)

    Original full-length Genbank format data (with sequence body)

    Original gbheader

   

5. Please specify the email address to which the outputs will be delivered:

 Email address *

choice of output 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

 

Three different SNP mapping modes:

<more information about the 3 modes>

BLAT created by Jim Kent, 2002 is used