ODDCOMP : Finds protein sequence regions with a biased composition (EMBOSS)
Some explanations about the options
input Section- 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)
advanced Section- Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz)
- The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid.
These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of 'Other' words.
required Section- 'compseq' file to use for expected word frequencies (-compdata)
- This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis.
- Window size to consider (e.g. 30 aa) (-window)
- This is the size of window in which to count.
Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here.
output Section- outfile (-outfile)
- This is the results file.
- 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.- enter either the name of a file or the actual data
Pise form generator version: 5.a (16 Dec 2002 11:54)
