Code for processing protein data
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GP_Reston_DaliLite_In.txt
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alignment.py
combAlign.py
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sGP_Reston_TM-align_In.txt

README.md

Protein

Code for processing protein data #############################################################################################

Module: combAlign.py

Version No.: 1.1

Programmer: Carol L. Ecale Zhou

Most recent update: 22 June 2015

Description: This code parses a set of pairwise structure- or sequence-based alignments

produced by TMalign (see http://zhanglab.ccmb.med.umich.edu/TM-align/), or Dali Lite

(see http://www.ebi.ac.uk/Tools/struture/dalilite/), and produces a gapped,

one-to-many, sequence alignment. Although any alignment program may be used to

produce the pairwise alignments, the format of the input to combAlign.py

should correspond to that produced by TMalign or Dali Lite. A reference fasta sequence

corresponding to the sequence or structure that has been compared to multiple other

sequences/structures, is used to construct the one-to-many alignment as output. Gaps may be

introduced into the reference sequence, as needed, to reflect deletions in the

reference with respect to any other structure or residues in the reference that were

not alignmed with any other sequence/structure according to the criteria applied in the

pairwise sequence/structure alignments.

Input requirements:

1) CombAlign.py takes as input a single text file, followed by the format (TM-align

or DaliLite), plus an optional positive integer.

2) The input file to combAlign.py comprises a single protein sequence in fasta format,

representing the reference sequence/structure, followed by a set of pairwise

alignments. In each pairwise alignment, the first sequence listed is from the

reference.

3) The second input parameter indicates the format used to perform the alignments.

Currently the acceptable formats are TM-align and DaliLite.

4) The third (optional) input parameter indicates the desired output alignment segment

length per line of output text. This parameter should be a positive number less than 250.

The default alignment segment length will be set to 80, if not provided by the user.

Programmer's notes:

This code can be easily modified to accommodate additional input file formats. Any

input file format should be parsed into the 'pairwise' data structure. If this is done

properly, then all subsequent calls to class alignment.py will function in exactly

the same way. To add additional formats, one need only add code under the 'ALIGN'

block (see line 332, beginning 'if ALIGN').

Copyright 2014 by Carol L. Ecale Zhou, Lawrence Livermore National Security. All Rights

Reserved. Permission to use, copy, modify, and distribute this software and its

documentation for educational, research, and not-for-profit purposes, without fee and

without a signed licensing agreement, is hereby granted, provided that the above

copyright notice, this paragraph and the following two paragraphs appear in all copies,

modifications, and distributions. Contact Office of XXXX, Lawrence Livermore National

Security for commercial licensing opportunities.

In no event shall LLNS be liable to any party for direct, indirect, special, incidental,

or consequential damages, including lost profits, arising out of the use of this

software and its documentation, even if LLNS has been advised of the possibility of

such damage.

LLNS disclaims any warranties, including, but no limited to, the implied

warranties of merchantability and fitness for a particular purpose. The software and

accompanying documentation, if any, provided hereunder is provided "as is", LLNS has

no obligation to provide maintenance, support, updates, enhancements, or modifications.

#############################################################################################