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Glimmer3 (version 3.02)

Genome Sequence:

Interpolated context model (ICM):

Set maximum overlap length:

Overlaps this short or shorter are ignored.

Set the minimum gene length to n nucleotides:

This does not include the bases in the stop codon.

Set threshold score for calling as gene:

If the in-frame score >= N, then the region is given a number and considered a potential gene.

Set the GC percentage of the independent model, i.e., the model of intergenic sequence:

If 0.0 specified, the GC percentage will be counted from the input file.

Assume linear rather than circular genome, i.e., no wraparound:

Don’t use the independent probability score column at all:

Using this option will produce more short gene predictions.

Also score orfs that extend off the end of the sequence(s):

Specify start codons as a comma-separated list:

Specify start codons as:

Use Genbank translation table to specify stop codons:

Report the classic glimmer table output:

Output a detailed gene prediction report as separate file:

What it does

This is the main program that makes gene predictions based on an interpolated context model (ICM).

The ICM can be generated with extracted CDS from related organisms (ICM builder). If you can't generate an ICM model you can use the non knowlegde-based Glimmer with a de novo prediction.

Input

Interpolated context model (ICM): Use the 'Glimmer ICM builder' tool to create one
Genome Sequence in FASTA format

Output

FASTA file with predicted proteins
Glimmer prediction file (optional)