GLIMMER : long-orfs - computes positions of the long orfs in the sequence (S. Salzberg)

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( = required, = conditionally required)

Genome sequence file : please enter either :

1. the name of a file:
2. or the actual data here:

(sequence format)



circular genome (-l)

minimum gene length (-g)

minimum overlap length (-o)

minimum overlap percent (-p)

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Some explanations about the options

Main parameters

enter either the name of a file or the actual data

if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)

OR you can type your data in the next area, or cut and paste it from another application.

(but not both)

circular genome (-l)

If the genome is not circular, do not allow genes to 'wrap around' the end of the genome.

minimum gene length (-g)

Minimum gene length is the length of the smallest fragment considered to be a gene. The length is measured from the first base of the start codon to the last base *before* the stop codon. This value can be specified when running the program with the -g option.

minimum overlap length (-o)

Minimum overlap length is a lower bound on the number of bases overlap between 2 genes that is considered a problem. Overlaps shorter than this are ignored.

minimum overlap percent (-p)

Minimum overlap percent is another lower bound on the number of bases overlap that is considered a problem. Overlaps shorter than this percentage of *both* genes are ignored. If you *DON'T* want to eliminate overlappinggenes, just use the -p 100 option.

Sequence format

The sequence will be automatically converted in the format needed for the program

providing you enter a sequence either:

in plain (raw) sequence format or in one of the following known formats:

IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW

You may enter in the text area a database entry code, or an accession number, in this form:

database:entry_name

or:

database:accession.