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README MARCOIL
This version might be outdated, please
check with the README included in the downlodable program's
distribution. Here first the instructions for downloading
and uncompressing.
MARCOIL
is a hidden MARkov model for predicting
existence and localisation of coiled-coil domains. Questions
and comments are welcome, email me at delorenzi@wehi.edu.au. Please report bugs.
INSTALLATION
After downloading a copy of the file
Marcoilcode.tar.gz in an appropriate directory,
extract with the commands
gunzip Marcoilcode.tar.gz
tar -xvf Marcoilcode.tar
This command creates a directory MARCOIL
containing all the files;
cd into the new directory and compile the
code by typing make. The makefile calls the gcc compiler and
the needed libraries. Various files should appear, including
the program MARCOIL and the most recent README
document.
Back to
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Nonetheless, in the following a
description on how to use Marcoil.
TESTING
From the MARCOIL directory, run the
program on the file SEQUENCES/seqfile2 by typing:
marcoil +cdlsS SEQUENCES/seqfile
and check out the appearance of four
result files in the subdirectory Outputs and their content.
The 5 options +cdlsS in the above command
do the following:
c the output file CompactProfile is
produced
d the output file Domains is produced
l the output file ProbList is produced
s the output file ProbPerState is
produced
S the protein Sequence is also written to
result files
Marcoil always rewrites the same output
files, so to keep results they have to be renamed or moved.
When the program has finished, a message is written to
stdout, as are some type of problems or errors, if
encountered.
RUNNING THE PROGRAM
Marcoil takes its parameters from a bunch
of files all located in the same subdirectory Inputs. This
should not be modified. If you run the PSSM algorithm by
using the -C option, then the option +s is inactive and the
output files are called CompactProfilePSSM, DomainsPSSM and
ProbListPSSM.
Running the program under UNIX or LINUX,
follow the usual rules for adresses. For example, start the
program from its directory with:
./ marcoil
the program looks for SEQUENCES/seqFile
and tries to use this file.
The output should be
self-explanatory.
INPUT FILES
Please use only fasta or multifasta
format, as only these were tested. The format is not checked
by the program and you could get false results.
The number of sequences is unlimited.
Only the 20 standard amino acids are
represented in the model, other letters are interpreted as
unknown amino acids.
Lowercase is converted to uppercase,
numbers, spaces, newlines, tabs and other special signs in
the sequence are ignored.
The program should be able to handle an
input with the folling schematic structure as examle:
> name of first sequence (name is
optional)
FIRST SEQUENCE perhaps with digits
61 continuation of sequence
>name of following sequence
SEQUENCE perhaps with s p a c e s and newlines
61 continuation of sequence
(EOF)
USAGE & COMMAND-LINE
OPTIONS
marcoil <-evwHLCI> <+cdlsS>
<-E filename> <-T filename> <-c number>
<+c number>
The order of the <...> blocks is
irrelevant.
OPTIONS
a) algorithmic / file / parameter options
[ -H ]
Read transition parameters from the file R3.transProbHigh
This is the default. We call it the MARCOIL-H predictor
[ -L ]
Read transition parameters from the file R3.transProbLow
This is what we call the MARCOIL-L predictor.
[ -E emfileName]
Read emission parameters from the user's file emfileName
[ -T trfileName]
Read transition parameters from the user's file
trfileName
[ -m trfileName]
Base emission parameters on the file R5.MTK or R5.MTIDK (if
-i), except state 0, based on R2.emissProb (or the -E
file)
[ -i ]
Use the MTIDK matrix instead of MTK (active only under -P or
-m) As file name the adress relative to the current
directory has to be used.
[ -P ]
Run the PSSM28 algorithm instead of MARCOIL, with the MTK
matrix (default, file R5.MTK) or the matrix specified with
the -E option The first is equivalent to COILS28 / MTK (up
to rounding errors)
b) numeric
[ -c probabilityCutoff]
Results are written only for positions with coiled-coil
probability equal or superior to probabilityCutoff
[ -t probabilityThreshold]
For the parsing, for defininf domain borders, use the
threshold probabilityThreshold instead of the default values
kParsingthreshold, defined in globals.h
c) output options
[ +d ] [ +l ] [ +m ] [ +s ] [ +S ]
Explained above.
[ -v ]
Run in verbose mode. A fair bit of output will be printed to
the screen to follow execution. Useful for tracing down
bugs.
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This page was last modified
Thursday, 24-Jan-2002 17:45:48 EST