* entries are required

1. Please give the name of a originally annotated sequence in Genbank format (preferably from Genbank or created by DNannotator, currently, some features, like CD, with joined multiple elements would not be transferred.  mRNA annotation will be converted into exons.  Annotation of repeats would not be transferred either.  If repeat information is needed, please use "locate repeat elements function")

Annotated Genbank data file *

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

  * Chromosome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y of latest version of UCSC freeze (be sure to select the correct one)

3. Adjustable parameters.

Annotation fashion: FAST MODE SLOW MODE

Additional parameters for BLAT-based annotation:

• Minimum sequence percentage of identity %

Additional parameters for BLAST-based annotation:

• E value  

For transfer the annotation,

• First filter

   

  @ Minimum percentage of identities for valid hits 95% 96% 97% 98% 99% 100%

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

  @ Minimum feature size bp

   

• Second filter

  @ Only the best matches will be used for annotation All hits above filter will be used for annotation

   

• For e-PCR-based annotation

  @ For annotation of features longer than bp, ePCR annotation will be used.

  @ In e-PCR annotation, the allowable size difference is bp, use bp end sequence of STS as e-PCR primers.

5. Choice of outputs:

    Show 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 

    Annotations failed to be transferred

    Duplicated features (possibly false positive due to homologs)

    Original BLAT output

    Data for the "custom track" of Genome Browser
         Name the track as
    Annotation evidence (compact parsed BLAT data)

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

    Original gbheader

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

 Email address *

choice of output in gzip compressed format: yes, zip it no, original data please

Your email box accepts message size limit of  1 MB 2 MB 4 MB 6 MB per message

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