DomFall - Bioplexity lectures code examples

DomFall - Bioplexity lectures code examlpes

DomFall is targeted to protein domain analysis, it comprises of several scripts for sequnce, pdb, and cvs data processing. These simple examples are available from the Bioplexity.org lectures web. The examples are based on the R-system, Python and Open-Bio projects.

DomFall scripts:

get for receiving sequences over network
mot for motif search along sequences
pdb for converting between pdb and cvs
con for conformation alignments
rot for rotating 3D structures
rms for computing rmsd between structures

get usage:
seqload.py database identifier filename seqload.pl module type identifier filename seqconv.py informat outformat infile outfile seqconv.pl informat outformat infile outfile

mot usage:
motfall.R domain.fa sequence.fa fits.csv results.csv

pdb usage:
pdb2csv.py -i file.pdb -t A|B|C|D -c chain_list -s start_residue -l last_residue csv2pdb.py -i file.csv [-h header.txt]

con usage:
confall.R points1.csv points2.csv output-centers.csv output-rotation.csv

rot usage:
rotfall.R centers.csv rotation.csv rank:1|2 points.csv output-rotated_points.csv

rms usage:
rmsdiff.R points1.csv points2.csv output-rmsd.csv