Glimmer : Search for genes (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)





Markov models for genes as produced by the program build-icm. : please enter either :

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

minimum gene length (-g)

Regard genome as circular (-l)

minimum overlap length (-o)

minimum overlap percent (-p)

threshold score for calling as gene (-t)

use first codon in orf as start codon (default, +f) or use ribosome-binding energy to choose start codon (-f)

Use this string as the ribosome binding pattern to find start codons. (-s)

Use independent probability score column (default, +r), or don't use it (-r)

Use 'weak' scores on potential genes at least n bases long (-w)

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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)

minimum gene length (-g)

Minimum gene length is the length of the smallest fragmentconsidered to be a gene. The length is measured from the first base of the start codon to the last base *before* the stop codon.

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 that 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* strings are ignored.

threshold score for calling as gene (-t)

Threshold score is the minimum in-frame score for a fragment to be considered a potential gene.

use first codon in orf as start codon (default, +f) or use ribosome-binding energy to choose start codon (-f)

Use first start codon indicates whether the first possible start codon is used or not. If not, the function Choose_Start is called to choose the start codon. Currently it computes hybridization energy between the string Ribosome_Pattern and the region in front of the start codon, and if this is above a threshold, that start site is chosen. The ribosome pattern string can be set by the -s option. Presumably function Choose_Start should be modified to do something cleverer. Currently used start codons are atg, gtg & ttg . These can be changed in the function Is_Start , but corresponding changes should be made in Choose_Start .

Use this string as the ribosome binding pattern to find start codons. (-s)

Use first start codon indicates whether the first possible start codon is used or not. If not, the function Choose_Start is called to choose the start codon. Currently it computes hybridization energy between the string Ribosome_Pattern and the region in front of the start codon, and if this is above a threshold, that start site is chosen. The ribosome pattern string can be set by the -s option. Presumably function Choose_Start should be modified to do something cleverer.

Use independent probability score column (default, +r), or don't use it (-r)

Use independent scores indicates whether the last column that scores each fragment using independent base probabilities is present.

Use 'weak' scores on potential genes at least n bases long (-w)

Weak scores ignore the independent model.

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.