AtGDB GeneSeqer Online Server

This server is a customized GeneSeqer site for splice threading of cDNAs/ESTs and target proteins into Arabidopsis genome segments. Follow steps 1 - 3 or click on Tutorial for more detailed instructions:

      Step 1:    Select Arabidopsis genomic DNA sequence
      Step 2:    Select or input cDNA/EST sequences
      Step 3:    Submit job

STEP 1:    Select Arabidopsis genomic DNA segment

Arabidopsis thaliana chromosome  12345
From position: to position: Strand: original reverse both

 

STEP 2:    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).

Database EST PUT cDNA
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All Plants
All Monocots
All Dicots
All Grasses
If you wish to have your species of interest added, please let us know by using our feedback function!
Aquilegia formosa x Aquilegia pubescens
Allium cepa
Avena sativa
Arabidopsis thaliana
Beta vulgaris
Coffea arabica
Coffea canephora
Citrus sinensis
Cucumis sativus
Ceratopteris richardii
Glycine max
Gossypium arboreum
Gossypium hirsutum
Helianthus annuus
Hordeum vulgare
Lotus japonicus
Solanum lycopersicum
Solanum pennellii
Marchantia polymorpha
Medicago sativa
Medicago truncatula
Mesembryanthemum crystallinum
Mimulus guttatus
Malus x domestica
Ipomoea nil
Oryza sativa
Phaseolus vulgaris
Physcomitrella patens
Pinus taeda
Pisum sativum
Populus tremula x Populus tremuloides
Prunus persica
Prunus avium
Prunus cerasus
Prunus avium x cerasus x canescens
Secale cereale
Solanum tuberosum
Sorghum bicolor
Sorghum propinquum
Triticum aestivum
Vitis vinifera
Zea mays
Database EST PUT cDNA
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 3:    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 4:    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.

     

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