PLOTCON : Plots the quality of conservation of a sequence alignment (EMBOSS)
Some explanations about the options
input Section- Sequences file to be read in (-msf)
- File containing a sequence alignment
- 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)
required Section- Window size (-winsize)
- Number of columns to average alignment quality over. The larger this value is, the smoother the plot will be.
output Section- Display as data (-data)
- Output the match data to a file instead of plotting it
- 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.- Sequences file to be read in (-msf)
Pise form generator version: 5.a (16 Dec 2002 11:54)
