PRETTYPLOT : Displays aligned sequences, with colouring and boxing (EMBOSS)
Some explanations about the options
consensus Section- Use alternative collisions routine (-alternative)
- Use alternative collisions routine
0) Normal collision check. (default)
1) checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred.
2) If another residue has a greater than or equal to matching score and these do not match then a collision has occurred.
3) Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured.
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)
advanced Section- Number of residues to be displayed on each line (-residuesperline)
- The number of residues to be displayed on each line
- shading (-shade)
- Set to BPLW for normal shading
so for pair = 1.5,1.0,0.5 and shade = BPLW
Residues score Colour
1.5 or over....... BLACK (B)
1.0 to 1.5 ....... BROWN (P)
0.5 to 1.0 ....... WHEAT (L)
under 0.5 ....... WHITE (W)
The only four letters allowed are BPLW, in any order.- 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.- Use alternative collisions routine (-alternative)
Pise form generator version: 5.a (16 Dec 2002 11:55)
