Module: peptide_dismatrix Description: Peptide Distance Matrix Generator Version: 1.1 Last Edit: 27/10/05

Copyright © 2005 Richard J. Edwards - See source code for GNU License Notice

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Imported modules: rje rje_aaprop rje_dismatrix rje_pam rje_seq

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See SLiMSuite Blog for further documentation. See rje for general commands.

Function

Generates distance matrix for input peptides.

Commandline

seqin=FILE : Peptide Sequence File
aaprop=FILE : Amino Acid property matrix file. [aaprop.txt]
outmatrix=X : Type for output matrix - text / mysql / phylip [Phylip]
delimit=X : Text delimiter for text or mysql file
method=X : Peptide Distance Method to use [ds_prop]
- ds_prop = Denis Shields distance using AA properties
- ds_id = Denis Shields distance using AA identity
- pam = ML PAM distance
- tot_prop = Summed difference across all properties in all residues
- best_prop = Minimum aligned property difference by circularising one peptide and sliding versus other