Glimmer : glimmer_extract - extracts subsequences corresponding to long orfs (S. Salzberg)

your e-mail

( = required, = conditionally required)

Genome sequence file : please enter either :

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

(sequence format)





list of start/stop pairs : please enter either :

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

skip the start codon (-skip)

minimum length of sequences (-l)

---

your e-mail

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)

list of start/stop pairs

The second command-line argument is the name of thecoordinate file. It must contain a list of pairs of positions in thefirst file, one per line. The format of each entry is:

'IDstring' 'start position' 'stop position'

This file should contain no other information, so if you're using the output of glimmer or long-orfs , you'll have to cut off header lines.

skip the start codon (-skip)

makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the default behaviour of the previous version of the program.

minimum length of sequences (-l)

makes the output omit any sequences shorter than n characters. n includes the 3 skipped characters if the -skip switch is on.

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.