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Usage instructions



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 FASTA 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 500,000 nucleotides.

2. Customize your run

  • Model organism
    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.

  • R-value cutoff
    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.




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