NRSCOPE : Converts redundant EMBL-format SCOP file to non-redundant one (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)
required Section- Gap insertion penalty (-gapopen)
- The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Allowed values: Floating point number from 1.0 to 100.0
- Gap extension penalty (-gapextend)
- The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Allowed values: Floating point number from 0.0 to 10.0
- enter either the name of a file or the actual data
Pise form generator version: 5.a (16 Dec 2002 11:54)
