PlantGDB GeneSeqer Online Server

STEP 1:    Select splice site model

Species (selects species-specific splice site model) Arabidopsis maize rice Medicago

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):

Select format: plain FASTA GenBank
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. You can supply your own EST/cDNA sequence as well as your own protein sequence to do the spliced alignment. However, your own EST/cDNA sequence can NOT be combined with our pre-processed databases (EST, PUT, or cDNA).

STEP 4:    Select alignment stringency level

Select "alignment stringency level" allowed user to select parameter to GeneSeqerWS. "Strict" invokes "-x 30 -y 45 -z 60", moderate "-x 16 -y 24 -z 48", and low "-x 12 -y 12 -z 30" argument to GeneSeqerWS.

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 instead. Selection of this option is advised in the rare case that output posting is slow due to server overload.

Click here to send the output to this email address:
HTML formatted output [default: simple text].This option will not work if your mailer wraps long lines.