GeneSeqer

GeneSeqer is a gene identification tool based on spliced alignment or "spliced threading" of ESTs with a genomic query sequence. Learn more.
For larger jobs, you might want to try the new Parallel GeneSeqer web interface.

Step 1: Select species-specific splice site model



Step 2: Input genomic DNA sequence

Sequences should be in the one-letter-code ({a,b,c,g,h,k,m,n,r,s,t,u,w,y}), upper or lower case; all other characters are ignored during input. Multiple sequence input is accepted in FASTA format (sequences separated by identifier lines of the form ">SQ;name_of_sequence comments") or in GenBank format.

Paste your genomic DNA sequence here:

... or upload your sequence file (specify file name):

... or type in the GenBank accession number of your sequence (its GenBank format sequence will be retrieved):

... or type in the chromosome number of your sequence:

Select format:

Sequence name: (optional, used in plain sequence format only)

From position: to position: Strand:

Step 3: Select or input cDNA/EST sequences
  Species name:
« « « Begin typing to search
Organism EST PUT cDNA HTC
OR paste your own EST/cDNA sequence(s) here in FASTA format
 ... and/or paste your own Protein sequence(s) here in FASTA format
... and/or upload your EST/cDNA sequence file (specify file name):
 ... and/or upload your Protein sequence file (specify file name):
Step 4: Select alignment stringency level


Step 5: Submit job

Select "Submit" to send the job to the server. By default, output will be posted to your browser. You may select to have the ouput sent to you by email instead. Selection of this option is advised in the rare case that output posting is slow due to server overload. If you (also) give us your email address, you will be notified when the job completes.

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