genseq.pl - Revision history

Edit: /* Options */

2009-07-29T02:44:20Z

Options

Edit: /* Options */

2009-07-29T02:43:49Z

Options

Edit: /* Options */

2009-07-29T02:41:41Z

Options

Edit: /* Description */

2009-07-29T02:39:29Z

Description

Edit: /* Description */

2009-07-29T02:38:57Z

Description

Feig at 14:20, 12 August 2006

2006-08-12T14:20:46Z

New page

__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="genseq.pl"></mmtsbToolUsage>

== Description ==

The main purpose of this script is to generate a MONSSTER amino acid
sequence file from a PDB file or sequence string but it can also
perform some other related functions. 
The input format is selected with the -pdb (PDB file, default),
-one (string consisting of one letter amino acid codes), or
-monsster (MONSSTER sequence file) options. If a file name is
specified input is read from that file, otherwise from standard input.
 
The output format is either a MONSSTER sequence file (default) or
a string of one letter amino acid codes. It is selected with
-out monsster or -out one, respectively. With
-out onesec secondary structure abbreviations are printed
along with the sequence. Using these
options a sequence file can be generated from a PDB file but it is also
possible to get an abbreviated sequence string from a sequence file, e.g.,
as shown in the examples below. 
If the PDB file is lacking part of the complete structure, as in typical
loop modeling applications, the sequence for the missing parts can be
given through the option -s. This option requires the first index
in the PDB structure and an abbreviated sequence string as a colon-separated
argument.
 
Further options are available to include secondary structure information
in the sequence file. If -dssp is specified the secondary structure
is taken from DSSP output. This requires the availability of a compiled
version of <A HREF="http://www.cmbi.kun.nl/gv/dssp/" TARGET=_new>DSSP</A> in the
MMTSB binary directory. With the option
-2ndpred a list of files containing output from common automated
secondary structure prediction programs can be provided. If more than file
is given a consensus prediction will be determined from all predictions.
Currently prediction outputs from the following programs are recognized:
PHD, SSpro, PSIpred, Jpred2, PSSP, PROF, Pred2ary.
Finally it is possible to set the secondary structure from a file containing
an abbreviated string with the option -2ndone.

== Options ==

; -help : usage information

== Examples ==

<mmtsbToolExample cmd="genseq.pl" set="/apps/mmtsb/bench/genseq.pl-test/test1"></mmtsbToolExample>

<mmtsbToolExample cmd="genseq.pl" set="/apps/mmtsb/bench/genseq.pl-test/test2"></mmtsbToolExample>

<mmtsbToolExample cmd="genseq.pl" set="/apps/mmtsb/bench/genseq.pl-test/test3"></mmtsbToolExample>

<mmtsbToolExample cmd="genseq.pl" set="/apps/mmtsb/bench/genseq.pl-test/test4"></mmtsbToolExample>

<mmtsbToolExample cmd="genseq.pl" set="/apps/mmtsb/bench/genseq.pl-test/test5"></mmtsbToolExample>

@@ Line 52: / Line 52: @@
 ; -2ndpred file[&#58;file...] : read secondary structure predictions from files
 ; -2ndone file : read one-letter secondary structure code from file
 == Examples ==

@@ Line 48: / Line 48: @@
 ; -one : read input as one-letter amino acid abbreviations
 ; -out one|onesec|sec|monsster : specify output format
-; -sel from:to : output only limited residue range
+; -sel from&#58;to : output only limited residue range
 == Examples ==

@@ Line 31: / Line 31: @@
 in the sequence file. If <B>-dssp</B> is specified the secondary structure
 is taken from DSSP output. This requires the availability of a compiled
-version of [ http://www.cmbi.kun.nl/gv/dssp/ DSSP] in the
+version of [http://www.cmbi.kun.nl/gv/dssp/ DSSP] in the
 MMTSB binary directory. With the option
 <B>-2ndpred</B> a list of files containing output from common automated

@@ Line 31: / Line 31: @@
 in the sequence file. If <B>-dssp</B> is specified the secondary structure
 is taken from DSSP output. This requires the availability of a compiled
-version of <A HREF="http://www.cmbi.kun.nl/gv/dssp/" TARGET=_new>DSSP</A> in the
+version of [ http://www.cmbi.kun.nl/gv/dssp/ DSSP] in the
 MMTSB binary directory. With the option
 <B>-2ndpred</B> a list of files containing output from common automated

@@ Line 44: / Line 44: @@
 ; -help : usage information
+; -pdb : read input in PDB format
 == Examples ==