USD Parallel GeneSeqer Online Service

Step 1 Select splice site model

You must choose a species-specific splice site model.

Species:

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 sequence:
	Upload your sequence:
	GenBank accession number of your sequence

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

From position: to position:

Strand: original reverse both

Step 3 Select or input cDNA/EST sequences

Spliced Alignment: The output will show an optimal threading of a significantly matching cDNA/EST sequence into the genomic DNA by aligning putative exons only and displaying putative introns as (long) gaps in the cDNA/EST.

If you wish to have your species of interest added, please let us know by using our feedback function!

Select a preprocessed EST database:

You may combine any number of the options specified below, however they cannot be combined with a preprocessed database listed above. Warning, uploading large files (around 50Mb) may cause your job to fail.

	Upload an EST/cDNA sequence file:
	... and/or paste EST/cDNA sequence(s):
	... and/or upload a Protein sequence file:
	... and/or paste Protein sequence(s):

Step 4 Select alignment stringency level

"Strict" sets the following parameters: "-x 30 -y 45 -z 60". Moderate sets the following parameters: "-x 16 -y 24 -z 48". Low sets the following parameters: "-x 12 -y 12 -z 30".

Select alignment stringency level: strict moderate low

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 as well.

Send the output to this email address:

Parallelism

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