1. Specify the input sequences
All the input sequences must be in one-letter nucleotide
code. The allowed alphabet (not case sensitive) is as follows:
A C G T and N (unknown)
All the other symbols will be converted to N before processing. The
sequences can be input in the following two ways:
Paste a single sequence (just the nucleotides) or a number of sequences in
format into the upper window of the main server page.
Select a FASTA
file on your local disk, either by typing the file name into the lower window
or by browsing the disk.
Both ways can be employed at the same time: all the specified sequences
will be processed. However, there may be at most 50 sequences and
1,000,000 nucleotides per submission; each sequence not more than
2. Customize your run
Select the model organism most closely related to the source organism
of your data. The pre-calculated EasyGene 1.2 predictions for the complete
genomes of the 138 organisms on the current model list can be downloaded
from the EasyGene site at BINF at the University of Copenhagen.
Each prediction is attributed with a significance score (R-value) indicating
how likely it is to be just a non-coding open reading frame rather than a real
gene. By default the server only shows gene predictions with R-values below
R=2. If more (and less certain!) predictions are wanted, one may enter
a higher R-value in the specified field. For small genes especially, it may be
a good idea to consider R-values up to around R=60.
Suboptimal gene starts
By default the server only shows the highest scoring start codons. If
alternative start codons are wanted, check the corresponding button.
3. Submit the job
Click on the "Submit"
button. The status of your job (either 'queued'
or 'running') will be displayed and constantly updated until it terminates and
the server output appears in the browser window.
At any time during the wait you may enter your e-mail address and simply leave
the window. Your job will continue; you will be notified by e-mail when it has
terminated. The e-mail message will contain the URL under which the results are
stored; they will remain on the server for 24 hours for you to collect them.