LIBGEN documentation


 


CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES



1.0 SUMMARY

Generates various types of discriminating elements for each alignment in a directory


2.0 INPUTS & OUTPUTS

LIBGEN reads a directory of alignments (typically DAF files - domain alignments file) and generates one of six types of profile for each alignment. Supported profiles include simple frequency matrices, Gribskov profiles, Hennikoff profiles, HMMs: hidden Markov models (HMMER package), HMMs (SAM-T2K package) and PSSMs: position-specific scoring matrices (PSIBLAST).

The base name of an input file is used as the base name for the output file. The paths and extensions for the alignment (input) and profile (output) files are provided by the user.


3.0 INPUT FILE FORMAT

The format of the domain alignment file is described in DOMAINALIGN documentation.
If another alignment file is used as input, all of the common file formats are supported.


4.0 OUTPUT FILE FORMAT

The format of the HMM files are described in the HMMER and SAM documentation.
The format of the profile file is described in the prophecy documentation. The format of the PSSM is described in the BLAST documentation.

Output files for usage example

File: 54894.disc

# Gribskov Protein Profile
# Columns are amino acids A->Z
# Last column is indel penalty
# Rows are alignment positions 1->n
Gribskov
Name		./54894.disc
Matrix		pprofile
Length		97
Max_score	1073.49
Threshold	75
Gap_open	3.00
Gap_extend	0.30
Consensus	GVEAIKNGTVIDHIPAGRAQIGFKLLGLFKLTETDQRITIGLNLPSSGELGRKDLIKIENTFISEDQADQLALYAPQATVNRIDNYEVVEKSRLSLP
2.40 0.00 0.80 2.40 2.00 -2.40 6.00 -0.80 -1.20 0.00 -0.40 -2.00 -1.20 1.60 0.00 1.20 0.80 -1.20 2.40 1.60 0.00 0.80 -4.00 0.00 -2.40 0.00 3.49 3.49
2.00 0.00 2.00 -2.00 -2.00 2.00 2.00 -3.00 11.00 0.00 -2.00 8.00 6.00 -3.00 0.00 1.00 -2.00 -3.00 -1.00 2.00 0.00 15.00 -8.00 0.00 -1.00 0.00 4.55 4.55
2.00 0.00 -3.00 6.40 9.40 -5.20 3.60 3.00 -2.00 0.00 3.80 -3.40 -1.40 3.80 0.00 2.00 4.20 3.20 4.40 1.60 0.00 -2.00 -3.40 0.00 -5.00 0.00 4.55 4.55
9.00 0.00 -0.60 3.00 3.00 -5.40 3.20 -0.20 -0.80 0.00 6.00 -1.80 0.80 2.80 0.00 3.40 2.80 1.40 3.20 3.20 0.00 0.40 -4.40 0.00 -4.20 0.00 4.55 4.55
0.00 0.00 2.00 -2.00 -2.00 6.00 -3.00 -3.00 15.00 0.00 -2.00 8.00 6.00 -3.00 0.00 -2.00 -3.00 -3.00 -1.00 2.00 0.00 11.00 -5.00 0.00 1.00 0.00 4.55 4.55
-1.20 0.00 -4.80 1.80 1.80 -5.60 -1.80 2.60 -2.40 0.00 12.20 -3.40 2.00 2.80 0.00 1.80 4.00 10.80 1.60 0.80 0.00 -2.40 5.80 0.00 -6.00 0.00 4.55 4.55
0.40 0.00 -1.20 2.80 2.40 -4.60 1.60 3.60 -2.60 0.00 5.20 -4.00 -1.00 7.00 0.00 2.00 3.00 6.60 4.60 1.00 0.00 -2.60 4.60 0.00 -3.60 0.00 4.55 4.55
6.00 0.00 2.00 6.00 5.00 -6.00 15.00 -2.00 -3.00 0.00 -1.00 -5.00 -3.00 4.00 0.00 3.00 2.00 -3.00 6.00 4.00 0.00 2.00 -10.00 0.00 -6.00 0.00 4.55 4.55
3.60 0.00 2.00 1.20 1.20 -2.00 3.60 -1.40 3.80 0.00 1.20 0.80 1.20 1.00 0.00 2.60 -1.20 -1.40 2.20 12.40 0.00 4.60 -6.40 0.00 -2.60 0.00 4.55 4.55
2.00 0.00 2.00 -2.00 -2.00 2.00 2.00 -3.00 11.00 0.00 -2.00 8.00 6.00 -3.00 0.00 1.00 -2.00 -3.00 -1.00 2.00 0.00 15.00 -8.00 0.00 -1.00 0.00 4.55 4.55
0.00 0.00 2.00 -2.00 -2.00 6.00 -3.00 -3.00 15.00 0.00 -2.00 8.00 6.00 -3.00 0.00 -2.00 -3.00 -3.00 -1.00 2.00 0.00 11.00 -5.00 0.00 1.00 0.00 4.55 4.55
3.00 0.00 -5.00 15.00 10.00 -10.00 6.00 4.00 -2.00 0.00 3.00 -5.00 -4.00 6.00 0.00 1.00 6.00 0.00 2.00 2.00 0.00 -2.00 -11.00 0.00 -5.00 0.00 4.55 4.55
-1.00 0.00 -1.00 4.00 4.00 -1.00 -2.00 15.00 -3.00 0.00 1.00 -2.00 -3.00 5.00 0.00 2.00 6.00 5.00 -2.00 -1.00 0.00 -3.00 -1.00 0.00 3.00 0.00 4.55 4.55
0.00 0.00 2.00 -2.00 -2.00 6.00 -3.00 -3.00 15.00 0.00 -2.00 8.00 6.00 -3.00 0.00 -2.00 -3.00 -3.00 -1.00 2.00 0.00 11.00 -5.00 0.00 1.00 0.00 4.55 4.55
5.00 0.00 1.00 1.00 1.00 -6.00 3.00 2.00 -2.00 0.00 1.00 -3.00 -2.00 0.00 0.00 15.00 3.00 3.00 4.00 3.00 0.00 1.00 -8.00 0.00 -8.00 0.00 4.55 4.55
4.00 0.00 0.80 0.80 0.80 -2.20 1.80 0.20 -0.40 0.00 0.20 -0.80 -0.40 0.40 0.00 4.00 1.00 0.00 1.60 1.40 0.00 0.60 -3.20 0.00 -2.20 0.00 2.38 2.38
2.40 0.00 0.80 2.40 2.00 -2.40 6.00 -0.80 -1.20 0.00 -0.40 -2.00 -1.20 1.60 0.00 1.20 0.80 -1.20 2.40 1.60 0.00 0.80 -4.00 0.00 -2.40 0.00 2.38 2.38
-1.20 0.00 -1.20 0.00 0.00 -2.00 -1.20 2.00 -1.20 0.00 3.20 -1.60 0.80 0.40 0.00 1.20 1.60 6.00 0.40 -0.40 0.00 -1.20 5.20 0.00 -2.40 0.00 2.38 2.38
15.00 0.00 3.00 3.00 3.00 -5.00 6.00 -1.00 0.00 0.00 0.00 -1.00 0.00 2.00 0.00 5.00 2.00 -3.00 4.00 4.00 0.00 2.00 -8.00 0.00 -3.00 0.00 4.55 4.55
-0.40 0.00 -5.40 0.00 1.20 1.00 -1.60 2.00 1.20 0.00 2.80 4.40 3.80 0.60 0.00 -0.40 5.00 1.40 -1.40 -0.80 0.00 0.80 1.60 0.00 -0.40 0.00 4.55 4.55
4.20 0.00 2.20 -0.20 -0.20 1.20 1.20 -2.20 8.60 0.00 -0.80 4.40 3.60 -1.00 0.00 1.00 -1.40 -2.60 0.80 5.00 0.00 8.20 -6.40 0.00 -1.00 0.00 4.55 4.55
4.00 0.00 0.40 2.40 2.20 -2.20 8.80 -2.40 1.60 0.00 -0.60 1.00 2.40 1.20 0.00 1.60 0.80 -2.00 2.80 2.80 0.00 5.40 -8.20 0.00 -4.00 0.00 4.55 4.55
-2.40 0.00 -3.20 -6.40 -4.00 12.00 -5.00 -1.80 8.60 0.00 -4.00 12.40 8.00 -4.20 0.00 -4.00 -4.20 -4.20 -3.00 -1.20 0.00 6.20 5.80 0.00 6.60 0.00 4.55 4.55
-0.60 0.00 -5.40 2.40 2.40 -5.80 -1.40 1.80 -2.20 0.00 13.60 -3.20 2.00 3.40 0.00 1.40 4.00 9.40 1.80 1.40 0.00 -2.20 3.40 0.00 -6.00 0.00 4.55 4.55
3.00 0.00 -1.80 -2.20 -1.40 5.40 -1.00 -2.20 8.40 0.00 -2.00 9.00 7.20 -2.40 0.00 -0.40 -1.00 -3.40 -1.20 1.20 0.00 8.80 -2.20 0.00 0.60 0.00 4.55 4.55
-1.00 0.00 -8.00 -5.00 -3.00 12.00 -5.00 -2.00 8.00 0.00 -3.00 15.00 12.00 -4.00 0.00 -3.00 -1.00 -4.00 -4.00 -1.00 0.00 8.00 5.00 0.00 3.00 0.00 4.55 4.55
4.00 0.00 2.00 3.80 3.40 -4.80 8.20 -1.40 -2.00 0.00 3.40 -4.20 -2.00 3.60 0.00 3.00 1.20 0.80 8.80 3.20 0.00 0.00 -2.60 0.00 -5.20 0.00 4.55 4.55
-0.80 0.00 -6.00 -4.40 -2.80 10.80 -4.60 -2.20 9.40 0.00 -2.80 13.60 10.80 -3.80 0.00 -2.80 -1.40 -3.80 -3.40 -0.40 0.00 8.60 3.00 0.00 2.60 0.00 4.55 4.55
-3.80 0.00 -2.80 -7.00 -4.20 10.40 -5.20 0.00 4.60 0.00 -2.60 9.40 5.80 -3.60 0.00 -3.60 -4.20 -0.80 -2.40 -2.20 0.00 2.20 10.80 0.00 7.20 0.00 4.55 4.55
2.80 0.00 -2.80 5.60 4.40 -6.80 4.40 1.20 -2.20 0.00 6.60 -3.80 -1.00 3.60 0.00 4.20 3.80 3.20 3.20 2.60 0.00 -0.60 -5.40 0.00 -6.20 0.00 4.55 4.55
0.60 0.00 -4.20 -2.60 -1.40 4.60 -2.00 -1.00 4.00 0.00 -0.60 7.80 7.40 -2.20 0.00 1.40 0.20 -0.60 -1.40 0.20 0.00 4.60 -0.20 0.00 -0.60 0.00 2.83 2.83
0.80 0.00 0.00 1.60 1.60 -2.40 0.60 3.60 -0.40 0.00 2.60 -1.60 -0.20 2.00 0.00 2.20 1.60 3.60 1.00 5.60 0.00 -0.40 0.00 0.00 -1.80 0.00 2.83 2.83
3.60 0.00 -1.40 6.80 8.40 -5.20 7.00 1.80 -2.20 0.00 2.20 -3.80 -2.60 6.40 0.00 1.80 3.40 -0.20 5.60 2.60 0.00 -1.20 -6.40 0.00 -4.20 0.00 4.55 4.55
2.40 0.00 2.80 2.20 3.20 -0.40 2.60 0.60 0.40 0.00 0.60 -1.20 -1.20 2.20 0.00 0.60 -0.60 -1.40 3.80 6.40 0.00 -0.00 -1.80 0.00 0.00 0.00 4.55 4.55
4.80 0.00 -1.60 7.80 5.60 -7.20 6.00 2.00 -2.00 0.00 2.60 -4.00 -1.80 3.80 0.00 2.60 4.00 1.80 3.00 2.20 0.00 -0.60 -5.40 0.00 -5.00 0.00 4.55 4.55
-1.00 0.00 -4.00 0.40 0.40 0.20 -2.00 4.00 -2.60 0.00 1.40 1.00 -0.80 1.60 0.00 -1.40 6.80 3.80 -0.80 -2.40 0.00 -3.00 2.20 0.00 1.60 0.00 4.55 4.55
-3.00 0.00 -3.00 0.00 0.00 -5.00 -3.00 5.00 -3.00 0.00 8.00 -4.00 2.00 1.00 0.00 3.00 4.00 15.00 1.00 -1.00 0.00 -3.00 13.00 0.00 -6.00 0.00 4.55 4.55


  [Part of this file has been deleted for brevity]

3.60 0.00 2.80 3.00 2.80 -4.20 6.40 -1.40 -1.60 0.00 4.00 -4.00 -2.00 3.40 0.00 3.20 0.60 1.60 10.60 3.00 0.00 -0.60 0.00 0.00 -4.80 0.00 4.55 4.55
1.20 0.00 0.40 1.20 1.00 -1.20 3.00 -0.40 -0.60 0.00 -0.20 -1.00 -0.60 0.80 0.00 0.60 0.40 -0.60 1.20 0.80 0.00 0.40 -2.00 0.00 -1.20 0.00 3.49 3.49
4.20 0.00 -4.20 5.80 7.80 -5.80 2.80 1.80 -1.60 0.00 7.20 -2.60 0.00 4.00 0.00 1.80 4.40 2.60 2.40 2.40 0.00 -1.20 -5.60 0.00 -5.00 0.00 4.55 4.55
-0.40 0.00 -5.20 -4.00 -2.40 8.00 -3.80 -2.60 8.60 0.00 -0.80 12.40 12.00 -3.40 0.00 -2.40 -1.00 -1.40 -3.00 0.00 0.00 7.80 -0.20 0.00 1.00 0.00 4.55 4.55
6.00 0.00 2.00 6.00 5.00 -6.00 15.00 -2.00 -3.00 0.00 -1.00 -5.00 -3.00 4.00 0.00 3.00 2.00 -3.00 6.00 4.00 0.00 2.00 -10.00 0.00 -6.00 0.00 4.55 4.55
-1.60 0.00 -1.20 0.40 0.40 -4.60 -1.20 3.60 -2.60 0.00 6.80 -4.00 1.00 1.40 0.00 3.20 3.00 12.20 3.80 -0.20 0.00 -2.60 11.00 0.00 -5.60 0.00 4.55 4.55
0.00 0.00 -6.00 3.00 3.00 -6.00 -1.00 1.00 -2.00 0.00 15.00 -3.00 2.00 4.00 0.00 1.00 4.00 8.00 2.00 2.00 0.00 -2.00 1.00 0.00 -6.00 0.00 4.55 4.55
3.00 0.00 -5.00 15.00 10.00 -10.00 6.00 4.00 -2.00 0.00 3.00 -5.00 -4.00 6.00 0.00 1.00 6.00 0.00 2.00 2.00 0.00 -2.00 -11.00 0.00 -5.00 0.00 4.55 4.55
-0.60 0.00 -4.00 -3.80 -2.60 9.60 -4.20 -2.40 10.80 0.00 -2.60 12.20 9.60 -3.60 0.00 -2.60 -1.80 -3.60 -2.80 0.20 0.00 9.20 1.00 0.00 2.20 0.00 4.55 4.55
0.00 0.00 -2.00 -3.20 -2.40 7.60 -2.80 -2.60 11.40 0.00 -2.40 10.80 8.40 -3.40 0.00 -1.80 -2.00 -3.40 -2.20 0.80 0.00 10.60 -1.60 0.00 1.40 0.00 4.55 4.55
0.00 0.00 -6.00 3.00 3.00 -6.00 -1.00 1.00 -2.00 0.00 15.00 -3.00 2.00 4.00 0.00 1.00 4.00 8.00 2.00 2.00 0.00 -2.00 1.00 0.00 -6.00 0.00 4.55 4.55
0.00 0.00 2.00 -2.00 -2.00 6.00 -3.00 -3.00 15.00 0.00 -2.00 8.00 6.00 -3.00 0.00 -2.00 -3.00 -3.00 -1.00 2.00 0.00 11.00 -5.00 0.00 1.00 0.00 4.55 4.55
3.00 0.00 -6.00 10.00 15.00 -6.00 5.00 4.00 -2.00 0.00 3.00 -3.00 -2.00 5.00 0.00 1.00 6.00 0.00 2.00 2.00 0.00 -2.00 -11.00 0.00 -5.00 0.00 4.55 4.55
3.00 0.00 -2.40 7.80 6.00 -6.20 6.60 3.40 -2.80 0.00 2.80 -4.40 -3.20 11.00 0.00 0.80 4.00 0.00 3.40 2.40 0.00 -1.80 -6.00 0.00 -2.80 0.00 4.55 4.55
0.80 0.00 2.60 -0.60 -0.60 0.80 0.20 0.60 2.60 0.00 0.80 1.00 1.40 0.20 0.00 0.40 -1.20 0.80 0.40 5.60 0.00 3.00 0.80 0.00 0.40 0.00 4.55 4.55
-2.60 0.00 -1.40 -5.80 -3.40 8.20 -3.40 -1.00 5.40 0.00 -1.00 8.20 4.60 -2.80 0.00 -3.20 -4.40 -2.00 -1.60 -1.00 0.00 3.80 5.80 0.00 6.40 0.00 4.55 4.55
0.60 0.00 -2.20 -2.60 -1.80 6.00 -2.60 -1.60 8.80 0.00 -1.80 8.60 6.80 -2.80 0.00 1.00 -1.00 -2.20 -1.20 1.00 0.00 7.80 -1.60 0.00 0.00 0.00 4.55 4.55
2.40 0.00 2.00 4.20 3.20 -4.80 4.20 0.60 -1.60 0.00 3.40 -4.20 -2.20 3.20 0.00 3.20 1.40 3.60 9.60 2.00 0.00 -1.60 2.20 0.00 -4.60 0.00 4.55 4.55
2.80 0.00 -6.00 9.20 13.20 -6.40 4.40 4.40 -2.20 0.00 3.20 -2.60 -1.60 4.80 0.00 1.40 7.80 0.80 1.40 1.40 0.00 -2.00 -9.80 0.00 -5.20 0.00 4.55 4.55
3.60 0.00 -3.20 7.20 5.20 -7.20 2.80 2.60 -1.80 0.00 5.80 -3.60 -0.80 3.80 0.00 2.20 4.40 4.00 2.20 1.80 0.00 -1.40 -3.20 0.00 -5.00 0.00 4.55 4.55
2.40 0.00 -5.80 8.60 8.60 -8.00 3.40 5.20 -2.60 0.00 3.60 -2.20 -1.20 4.60 0.00 2.20 11.40 2.40 0.20 0.20 0.00 -2.00 -7.40 0.00 -5.60 0.00 4.55 4.55
6.60 0.00 0.40 -0.60 -0.20 1.20 2.20 -2.00 6.00 0.00 -1.40 5.80 4.80 -1.20 0.00 1.80 -0.20 -3.20 0.40 2.20 0.00 8.40 -5.40 0.00 -1.00 0.00 4.55 4.55
3.00 0.00 -2.60 9.60 8.40 -6.80 5.40 3.00 -2.00 0.00 3.00 -4.20 -3.20 7.00 0.00 1.40 4.20 0.40 4.80 2.20 0.00 -2.00 -6.60 0.00 -4.00 0.00 4.55 4.55
1.00 0.00 -4.80 1.60 2.00 -1.60 -0.00 1.60 2.20 0.00 3.60 3.60 4.00 1.00 0.00 1.00 6.20 1.80 -1.00 0.20 0.00 3.40 -2.40 0.00 -3.20 0.00 4.55 4.55
-0.80 0.00 -6.00 -4.40 -2.80 10.80 -4.60 -2.20 9.40 0.00 -2.80 13.60 10.80 -3.80 0.00 -2.80 -1.40 -3.80 -3.40 -0.40 0.00 8.60 3.00 0.00 2.60 0.00 4.55 4.55
11.00 0.00 2.60 3.40 3.20 -4.80 7.40 -1.20 -0.20 0.00 0.20 -1.80 -0.60 2.40 0.00 4.20 1.40 -2.60 4.20 6.20 0.00 2.00 -8.00 0.00 -3.60 0.00 4.55 4.55
-0.80 0.00 -6.00 -4.40 -2.80 10.80 -4.60 -2.20 9.40 0.00 -2.80 13.60 10.80 -3.80 0.00 -2.80 -1.40 -3.80 -3.40 -0.40 0.00 8.60 3.00 0.00 2.60 0.00 4.55 4.55
-1.80 0.00 6.80 -3.80 -3.80 10.20 -4.80 0.60 6.60 0.00 -4.40 5.00 1.80 -1.80 0.00 -5.60 -4.80 -4.80 -2.80 -1.00 0.00 3.80 4.60 0.00 9.40 0.00 4.55 4.55
15.00 0.00 3.00 3.00 3.00 -5.00 6.00 -1.00 0.00 0.00 0.00 -1.00 0.00 2.00 0.00 5.00 2.00 -3.00 4.00 4.00 0.00 2.00 -8.00 0.00 -3.00 0.00 4.55 4.55
5.00 0.00 1.00 1.00 1.00 -6.00 3.00 2.00 -2.00 0.00 1.00 -3.00 -2.00 0.00 0.00 15.00 3.00 3.00 4.00 3.00 0.00 1.00 -8.00 0.00 -8.00 0.00 4.55 4.55
2.60 0.00 -1.00 4.80 4.60 -5.20 4.60 4.60 -2.60 0.00 2.00 -2.60 -1.80 4.00 0.00 3.00 7.40 2.20 3.40 0.80 0.00 -1.20 -3.60 0.00 -3.80 0.00 4.55 4.55
15.00 0.00 3.00 3.00 3.00 -5.00 6.00 -1.00 0.00 0.00 0.00 -1.00 0.00 2.00 0.00 5.00 2.00 -3.00 4.00 4.00 0.00 2.00 -8.00 0.00 -3.00 0.00 4.55 4.55
4.00 0.00 2.00 2.00 2.00 -3.00 4.00 -1.00 2.00 0.00 2.00 -1.00 0.00 2.00 0.00 3.00 -1.00 -1.00 3.00 15.00 0.00 2.00 -6.00 0.00 -3.00 0.00 4.55 4.55
0.20 0.00 1.40 -3.60 -2.80 5.40 -0.60 -2.60 10.80 0.00 -2.80 8.80 5.80 -3.40 0.00 -1.00 -3.40 -3.40 -1.40 1.00 0.00 11.60 -3.40 0.00 2.20 0.00 4.55 4.55
2.00 0.00 -3.00 6.00 5.00 -5.00 4.00 5.00 -3.00 0.00 4.00 -4.00 -3.00 15.00 0.00 0.00 4.00 1.00 3.00 2.00 0.00 -3.00 -3.00 0.00 -1.00 0.00 4.55 4.55
-0.40 0.00 -1.60 0.40 0.40 -2.00 -1.00 2.00 3.40 0.00 3.20 1.40 3.20 0.00 0.00 1.60 3.60 5.60 -0.20 0.20 0.00 3.60 1.60 0.00 -3.60 0.00 4.55 4.55
0.00 0.00 2.00 -2.00 -2.00 6.00 -3.00 -3.00 15.00 0.00 -2.00 8.00 6.00 -3.00 0.00 -2.00 -3.00 -3.00 -1.00 2.00 0.00 11.00 -5.00 0.00 1.00 0.00 4.55 4.55
1.80 0.00 -5.00 10.00 10.00 -7.40 3.80 4.20 -2.20 0.00 4.00 -4.00 -2.00 4.60 0.00 1.40 5.60 3.00 1.80 1.40 0.00 -2.20 -6.20 0.00 -5.20 0.00 4.55 4.55
2.40 0.00 -3.80 9.60 7.00 -7.00 4.80 4.60 -2.60 0.00 3.60 -4.40 -3.40 11.40 0.00 0.40 4.80 0.60 2.60 2.00 0.00 -2.60 -6.20 0.00 -2.60 0.00 4.55 4.55
-3.00 0.00 10.00 -5.00 -5.00 13.00 -6.00 3.00 1.00 0.00 -6.00 3.00 -1.00 -1.00 0.00 -8.00 -6.00 -6.00 -4.00 -3.00 0.00 -1.00 11.00 0.00 15.00 0.00 4.55 4.55
2.20 0.00 -4.40 6.20 9.20 -4.40 3.20 2.00 0.60 0.00 4.40 -0.80 0.40 3.20 0.00 1.00 4.00 1.00 1.40 2.00 0.00 1.40 -8.00 0.00 -4.40 0.00 4.55 4.55
2.00 0.00 2.00 -2.00 -2.00 2.00 2.00 -3.00 11.00 0.00 -2.00 8.00 6.00 -3.00 0.00 1.00 -2.00 -3.00 -1.00 2.00 0.00 15.00 -8.00 0.00 -1.00 0.00 4.55 4.55
2.40 0.00 2.00 -1.20 -1.20 1.00 2.40 -2.60 9.20 0.00 -1.20 6.20 4.80 -2.00 0.00 1.40 -1.80 -2.60 -0.20 4.60 0.00 12.40 -7.60 0.00 -1.40 0.00 4.55 4.55
3.60 0.00 -2.80 7.00 8.60 -6.00 7.80 1.00 -2.40 0.00 3.80 -3.80 -1.60 4.40 0.00 1.80 4.00 0.40 3.60 2.80 0.00 -0.40 -8.20 0.00 -5.60 0.00 4.55 4.55
0.00 0.00 -6.00 3.00 3.00 -6.00 -1.00 1.00 -2.00 0.00 15.00 -3.00 2.00 4.00 0.00 1.00 4.00 8.00 2.00 2.00 0.00 -2.00 1.00 0.00 -6.00 0.00 4.55 4.55
1.20 0.00 0.60 -0.60 -0.20 0.60 1.20 -0.80 2.80 0.00 1.40 2.20 2.80 0.00 0.00 1.80 -0.20 2.00 5.20 1.20 0.00 3.60 3.20 0.00 -2.40 0.00 4.55 4.55
1.60 0.00 -2.00 2.00 2.00 -4.40 -0.60 5.00 -2.20 0.00 6.40 -2.80 0.60 2.60 0.00 2.80 4.00 8.00 1.20 0.60 0.00 -1.80 3.60 0.00 -3.60 0.00 4.55 4.55
1.40 0.00 -4.40 -2.60 -1.40 4.80 -1.80 -0.40 4.00 0.00 -1.40 7.80 6.40 -2.40 0.00 4.20 0.60 -1.20 -0.80 0.60 0.00 5.20 -0.20 0.00 -1.40 0.00 4.55 4.55
2.60 0.00 -1.20 4.60 5.60 -5.20 3.60 1.40 -1.80 0.00 5.20 -3.00 -1.20 3.80 0.00 2.60 4.60 2.80 6.60 1.80 0.00 -1.60 -1.80 0.00 -5.00 0.00 4.55 4.55
-0.40 0.00 -6.00 -4.40 -2.80 10.00 -3.60 -2.20 8.60 0.00 -2.80 13.60 10.80 -3.80 0.00 -2.20 -1.20 -3.80 -3.40 -0.40 0.00 9.40 2.40 0.00 2.20 0.00 4.55 4.55
5.00 0.00 1.00 1.00 1.00 -6.00 3.00 2.00 -2.00 0.00 1.00 -3.00 -2.00 0.00 0.00 15.00 3.00 3.00 4.00 3.00 0.00 1.00 -8.00 0.00 -8.00 0.00 4.55 4.55

File: 55074.disc

# Gribskov Protein Profile
# Columns are amino acids A->Z
# Last column is indel penalty
# Rows are alignment positions 1->n
Gribskov
Name		./55074.disc
Matrix		pprofile
Length		257
Max_score	1759.18
Threshold	75
Gap_open	3.00
Gap_extend	0.30
Consensus	GVEAIKNGTVIDHIPAGRAQIGFKLLGLFKLTETDQRITIGLNLPSSGELGRKDLIKIENTFISEDQADQLALYAPQATVNRIDNYEVVEKSRLSLPMMFHFRAFKKKKFDDVTILFADIVGFTAICAQCSEGPDELIDMLNELFGRFDELCGEPHYLDCYKIKTIGDAYCCASGLHEKRADHAFCCAEMALKMIEAIEEVMDPDGDALDDSXREFEEQRAEGECEXTPPTAHMDPEVXSMLWENIKMRIGIHSGLSVLAGVLGVRKPRYDLWGNDVNLANKMESGGVAGRIHISEATYRLLSAEDGKDYEVEAGCGDERAGAGAVADPIKGFKILLIPSRNFAALRLDREXFD
0.00 0.00 -1.00 -0.67 -0.33 0.83 -0.50 -0.50 1.00 0.00 0.33 2.00 2.50 -0.50 0.00 -0.33 0.00 0.33 -0.50 0.00 0.00 1.00 -0.50 0.00 -0.17 0.00 1.13 1.13
0.00 0.00 -1.00 -0.67 -0.33 0.83 -0.50 -0.50 1.00 0.00 0.33 2.00 2.50 -0.50 0.00 -0.33 0.00 0.33 -0.50 0.00 0.00 1.00 -0.50 0.00 -0.17 0.00 1.13 1.13
-0.50 0.00 -0.33 -1.00 -0.50 2.67 -0.83 0.17 3.00 0.00 -0.67 2.67 1.33 1.17 0.00 -1.33 -1.17 -1.17 -0.17 0.17 0.00 1.67 0.67 0.00 2.17 0.00 1.13 1.13
0.17 0.00 -0.33 1.33 1.17 -0.00 -0.17 2.83 1.50 0.00 0.50 0.33 0.00 2.83 0.00 0.00 1.17 0.50 0.00 0.50 0.00 0.83 -1.50 0.00 0.50 0.00 1.13 1.13
-0.50 0.00 -1.67 -0.17 0.33 0.67 -0.50 0.83 0.17 0.00 2.17 0.83 0.67 2.33 0.00 -0.83 0.00 0.67 0.33 0.17 0.00 -0.50 1.67 0.00 1.00 0.00 1.13 1.13
-1.00 0.00 -0.67 -0.33 -0.33 -0.67 -1.50 1.17 1.50 0.00 2.33 0.00 1.67 -0.17 0.00 0.67 0.83 4.50 0.17 0.00 0.00 0.83 3.50 0.00 -1.83 0.00 1.13 1.13
2.83 0.00 2.33 -0.17 -0.17 0.33 0.50 0.67 -0.17 0.00 -0.83 -0.17 -0.50 0.17 0.00 2.00 -0.17 -1.00 0.67 0.67 0.00 0.33 -0.83 0.00 0.67 0.00 1.13 1.13
0.00 0.00 0.33 -1.83 -1.17 2.50 -1.00 -0.33 3.17 0.00 -1.17 2.83 1.50 -1.33 0.00 1.17 -1.33 -0.83 0.00 0.33 0.00 2.33 -0.17 0.00 1.00 0.00 1.13 1.13
-0.17 0.00 -0.33 0.67 0.67 -0.17 -0.83 1.67 -0.67 0.00 2.17 -0.17 0.17 1.17 0.00 -0.67 2.17 1.00 -0.50 -0.33 0.00 -0.83 1.17 0.00 0.50 0.00 1.13 1.13
0.67 0.00 -2.00 0.67 1.00 -1.67 0.17 -0.50 0.17 0.00 5.67 0.33 2.67 1.33 0.00 0.67 1.17 3.17 2.67 1.17 0.00 0.17 0.33 0.00 -2.83 0.00 1.13 1.13
0.33 0.00 -4.50 3.67 4.50 -5.17 0.33 2.83 -2.00 0.00 7.50 -2.33 0.67 3.00 0.00 1.50 5.50 5.83 1.00 0.67 0.00 -1.83 -0.17 0.00 -4.83 0.00 4.55 4.55
1.33 0.00 -3.50 3.83 3.67 -5.33 0.83 5.00 -2.50 0.00 6.67 -2.67 -0.67 5.33 0.00 3.67 6.00 4.83 1.33 1.17 0.00 -1.83 -2.50 0.00 -4.00 0.00 4.55 4.55
-1.17 0.00 0.17 -2.67 -1.33 5.33 -2.17 1.50 4.33 0.00 -1.83 4.83 2.17 -1.00 0.00 -1.50 -2.33 -1.50 -1.00 1.67 0.00 2.33 2.00 0.00 4.50 0.00 4.55 4.55
3.17 0.00 -3.33 12.00 9.50 -8.17 5.83 3.00 -1.83 0.00 2.83 -4.50 -3.50 5.33 0.00 1.50 4.83 0.17 4.17 2.17 0.00 -1.83 -8.67 0.00 -4.83 0.00 4.55 4.55
3.17 0.00 -2.17 6.67 6.50 -6.33 4.33 3.17 -2.17 0.00 2.83 -3.33 -2.33 5.50 0.00 4.00 5.50 1.50 4.17 1.83 0.00 -1.50 -5.83 0.00 -4.83 0.00 4.55 4.55
2.67 0.00 2.00 -0.67 -0.83 0.67 4.17 -2.83 8.67 0.00 -1.83 5.83 4.50 -1.83 0.00 1.33 -1.33 -3.00 0.17 2.33 0.00 12.83 -8.33 0.00 -1.83 0.00 4.55 4.55
4.33 0.00 3.33 2.67 2.50 -3.50 6.50 -1.50 0.17 0.00 1.50 -2.67 -1.50 2.67 0.00 3.33 -0.50 -0.67 7.50 9.17 0.00 1.00 -3.67 0.00 -3.83 0.00 4.55 4.55
0.17 0.00 -2.33 -3.17 -2.17 6.00 -2.50 -2.83 10.17 0.00 -0.83 10.50 10.00 -3.17 0.00 -1.67 -1.50 -1.50 -2.17 0.83 0.00 9.50 -3.17 0.00 0.33 0.00 4.55 4.55
-0.67 0.00 -4.67 -4.00 -2.67 10.00 -4.33 -2.33 10.33 0.00 -2.67 12.67 10.00 -3.67 0.00 -2.67 -1.67 -3.67 -3.00 0.00 0.00 9.00 1.67 0.00 2.33 0.00 4.55 4.55
-5.00 0.00 -1.00 -10.00 -6.00 15.00 -6.00 -1.00 6.00 0.00 -6.00 12.00 5.00 -5.00 0.00 -6.00 -8.00 -5.00 -3.00 -3.00 0.00 2.00 12.00 0.00 13.00 0.00 4.55 4.55
9.50 0.00 3.83 2.50 2.50 -4.00 5.67 -1.33 0.00 0.00 1.00 -2.00 -1.00 2.33 0.00 4.33 0.50 -1.33 7.50 5.50 0.00 1.00 -4.00 0.00 -3.33 0.00 4.55 4.55
3.17 0.00 -3.17 12.83 8.67 -8.83 6.00 3.00 -1.83 0.00 2.83 -4.83 -3.83 5.50 0.00 1.50 4.83 0.17 4.17 2.17 0.00 -1.83 -8.67 0.00 -4.83 0.00 4.55 4.55
0.00 0.00 2.00 -2.00 -2.00 6.00 -3.00 -3.00 15.00 0.00 -2.00 8.00 6.00 -3.00 0.00 -2.00 -3.00 -3.00 -1.00 2.00 0.00 11.00 -5.00 0.00 1.00 0.00 4.55 4.55
2.33 0.00 -0.67 2.00 3.67 -0.67 3.00 -0.67 6.67 0.00 -0.33 4.33 3.33 -0.33 0.00 1.00 0.67 -2.00 0.00 2.00 0.00 9.33 -9.00 0.00 -2.33 0.00 4.55 4.55
5.00 0.00 1.83 5.33 4.50 -5.33 11.67 -0.83 -2.67 0.00 0.33 -4.67 -3.00 5.67 0.00 2.67 1.83 -1.67 7.00 3.50 0.00 0.67 -6.67 0.00 -4.83 0.00 4.55 4.55
-3.50 0.00 0.17 -8.00 -4.67 12.00 -4.00 -1.17 4.83 0.00 -4.67 9.33 3.67 -3.67 0.00 -4.33 -6.83 -4.00 0.00 -2.00 0.00 1.50 10.50 0.00 10.17 0.00 4.55 4.55
4.00 0.00 2.67 2.00 2.00 -3.00 4.33 -1.17 1.50 0.00 2.00 -1.50 -0.50 2.17 0.00 3.17 -1.00 -0.67 5.00 13.00 0.00 1.50 -4.50 0.00 -3.17 0.00 4.55 4.55
8.67 0.00 0.50 4.00 4.83 -5.00 4.67 0.00 -0.83 0.00 3.33 -2.17 -0.50 3.00 0.00 3.50 2.50 0.00 5.17 3.17 0.00 0.17 -5.17 0.00 -4.00 0.00 4.55 4.55
-1.17 0.00 -3.17 -4.67 -3.00 9.33 -4.17 -2.33 9.67 0.00 -2.33 11.67 9.33 -3.67 0.00 -3.00 -2.67 -2.83 -2.67 -0.17 0.00 7.67 1.50 0.00 3.33 0.00 4.55 4.55
2.33 0.00 6.17 -3.50 -3.83 2.50 0.00 -0.50 -0.17 0.00 -2.50 -2.17 -3.17 -0.83 0.00 -0.83 -3.67 -0.17 5.00 0.33 0.00 -0.67 -0.50 0.00 6.50 0.00 4.55 4.55
9.33 0.00 2.50 3.83 4.67 -4.50 5.83 -0.50 -0.67 0.00 1.17 -2.33 -1.33 2.83 0.00 4.00 1.67 -1.17 7.33 3.33 0.00 0.33 -4.83 0.00 -3.67 0.00 4.55 4.55
4.33 0.00 -4.00 6.17 6.83 -6.67 3.50 4.33 -2.33 0.00 3.17 -1.83 -0.83 5.67 0.00 2.50 9.50 1.67 1.00 0.83 0.00 -1.50 -6.17 0.00 -4.50 0.00 4.55 4.55
1.83 0.00 6.00 -1.00 -1.67 -2.33 1.50 0.50 0.17 0.00 0.17 -5.17 -3.17 1.67 0.00 0.67 -1.67 0.00 3.83 1.67 0.00 0.17 -6.33 0.00 3.83 0.00 4.55 4.55
2.00 0.00 4.17 1.17 1.17 0.00 2.00 2.00 -0.00 0.00 0.50 -1.50 -1.67 2.33 0.00 1.33 -0.67 -0.17 5.00 5.33 0.00 -0.33 0.67 0.00 0.67 0.00 4.55 4.55
0.50 0.00 -1.00 1.67 2.50 -1.00 0.83 0.67 -0.33 0.00 0.50 -0.50 -0.33 0.83 0.00 0.17 1.00 0.00 0.33 0.33 0.00 -0.33 -1.83 0.00 -0.83 0.00 2.83 2.83
1.00 0.00 0.33 1.00 0.83 -1.00 2.50 -0.33 -0.50 0.00 -0.17 -0.83 -0.50 0.67 0.00 0.50 0.33 -0.50 1.00 0.67 0.00 0.33 -1.67 0.00 -1.00 0.00 2.83 2.83
8.50 0.00 1.83 2.50 2.33 -5.67 6.00 0.33 -1.50 0.00 0.33 -2.67 -1.50 1.33 0.00 9.67 2.50 0.00 4.33 3.50 0.00 1.50 -8.33 0.00 -6.00 0.00 4.55 4.55


  [Part of this file has been deleted for brevity]

2.50 0.00 -1.83 3.50 2.67 -4.33 1.33 1.50 -1.17 0.00 4.33 -2.17 0.00 2.17 0.00 1.67 2.67 3.33 1.50 1.17 0.00 -0.83 -0.83 0.00 -3.33 0.00 0.27 0.27
0.50 0.00 -2.50 3.33 5.00 -2.83 1.17 2.17 -1.17 0.00 2.33 -1.67 -0.33 1.83 0.00 0.83 2.67 2.50 0.83 0.50 0.00 -1.17 -1.50 0.00 -2.67 0.00 0.27 0.27
0.50 0.00 -0.83 2.50 1.67 -1.67 1.00 0.67 -0.33 0.00 0.50 -0.83 -0.67 1.00 0.00 0.17 1.00 0.00 0.33 0.33 0.00 -0.33 -1.83 0.00 -0.83 0.00 0.27 0.27
0.50 0.00 -0.17 1.00 0.83 -1.83 2.00 0.50 -1.00 0.00 1.17 -1.50 -0.17 0.83 0.00 1.00 1.00 2.00 1.17 0.50 0.00 -0.17 0.50 0.00 -2.00 0.00 0.27 0.27
0.00 0.00 -1.00 0.50 0.50 -1.00 -0.17 0.17 -0.33 0.00 2.50 -0.50 0.33 0.67 0.00 0.17 0.67 1.33 0.33 0.33 0.00 -0.33 0.17 0.00 -1.00 0.00 0.27 0.27
0.83 0.00 -1.83 3.50 2.67 -3.00 1.33 1.67 -0.83 0.00 1.17 -1.00 -0.67 1.67 0.00 0.67 3.50 0.67 0.17 0.17 0.00 -0.67 -2.67 0.00 -1.83 0.00 0.27 0.27
-1.00 0.00 3.67 -2.00 -2.00 5.33 -2.50 0.50 2.83 0.00 -2.33 2.33 0.67 -0.83 0.00 -3.00 -2.50 -2.50 -1.50 -0.67 0.00 1.50 2.83 0.00 5.17 0.00 0.27 0.27
1.50 0.00 -2.83 5.83 6.67 -3.67 2.67 2.00 -1.00 0.00 1.50 -1.83 -1.33 2.67 0.00 0.50 3.00 0.00 1.00 1.00 0.00 -1.00 -5.50 0.00 -2.50 0.00 0.27 0.27
0.67 0.00 -0.33 -1.33 -1.00 1.50 0.17 -1.50 4.67 0.00 -0.33 4.67 4.50 -1.50 0.00 0.00 -0.67 -0.67 -0.83 0.67 0.00 6.00 -3.17 0.00 -0.50 0.00 0.27 0.27
1.67 0.00 -1.67 3.67 5.33 -2.50 2.33 1.17 -0.33 0.00 1.33 -1.17 -0.67 2.00 0.00 0.83 1.83 -0.17 1.17 3.17 0.00 -0.33 -4.67 0.00 -2.17 0.00 0.27 0.27
3.83 0.00 -0.17 3.17 2.33 -3.50 2.50 0.83 -0.67 0.00 0.67 -1.50 -1.00 1.33 0.00 3.50 1.83 0.00 1.67 1.50 0.00 0.17 -4.50 0.00 -2.67 0.00 0.27 0.27
1.83 0.00 -0.67 1.17 1.17 0.00 4.17 -1.00 0.33 0.00 -0.83 0.83 1.00 0.67 0.00 0.50 0.50 -1.67 1.33 1.17 0.00 2.00 -2.50 0.00 -1.50 0.00 0.27 0.27
0.50 0.00 1.50 -0.33 -0.50 -1.17 0.17 0.00 0.00 0.00 1.50 -1.83 -0.67 0.17 0.00 0.33 -0.33 0.83 1.33 0.67 0.00 0.00 -1.83 0.00 0.67 0.00 0.27 0.27
2.33 0.00 1.00 1.67 1.33 -1.67 5.33 -1.17 0.83 0.00 -0.67 -0.33 0.00 0.83 0.00 1.17 0.33 -1.50 1.83 1.67 0.00 3.17 -4.67 0.00 -2.17 0.00 0.27 0.27
2.17 0.00 -0.17 3.83 2.83 -3.17 4.17 0.17 -0.50 0.00 0.67 -1.83 -1.17 2.00 0.00 1.17 1.17 -0.67 1.83 3.50 0.00 0.33 -4.50 0.00 -2.33 0.00 0.27 0.27
1.00 0.00 -2.00 3.33 5.00 -2.00 1.67 1.33 -0.67 0.00 1.00 -1.00 -0.67 1.67 0.00 0.33 2.00 0.00 0.67 0.67 0.00 -0.67 -3.67 0.00 -1.67 0.00 0.27 0.27
-0.67 0.00 -0.67 -0.33 -0.33 -1.33 -0.67 1.17 0.83 0.00 2.33 0.00 1.67 -0.17 0.00 1.17 1.00 4.50 0.17 0.00 0.00 1.50 3.00 0.00 -2.17 0.00 0.27 0.27
3.17 0.00 0.33 1.17 1.00 -1.33 2.00 0.17 1.33 0.00 0.33 0.50 0.50 2.33 0.00 1.00 0.67 -0.83 1.00 1.33 0.00 2.33 -3.17 0.00 -0.83 0.00 0.27 0.27
0.83 0.00 -1.00 0.17 0.33 1.00 1.67 -0.67 0.83 0.00 -0.67 1.67 1.50 0.00 0.00 0.00 0.17 -1.17 0.33 0.50 0.00 1.67 -0.83 0.00 -0.50 0.00 0.27 0.27
2.33 0.00 -1.00 1.50 1.50 -3.00 0.83 1.67 -1.00 0.00 2.00 -1.00 0.33 1.17 0.00 1.83 3.50 2.67 0.67 0.33 0.00 -0.50 0.00 0.00 -2.50 0.00 0.27 0.27
1.17 0.00 3.00 0.50 0.33 0.67 2.50 -0.17 -0.50 0.00 -0.83 -1.00 -1.17 1.00 0.00 -0.17 -0.83 -1.33 2.83 0.67 0.00 0.00 0.67 0.00 0.83 0.00 0.27 0.27
2.33 0.00 -0.83 -0.33 0.00 1.17 0.17 -0.50 1.33 0.00 -0.50 2.33 2.00 -0.33 0.00 0.33 0.17 -1.17 0.00 0.50 0.00 1.67 -0.50 0.00 0.00 0.00 0.27 0.27
0.67 0.00 -0.33 -0.17 -0.17 -0.33 0.50 -0.83 3.33 0.00 1.83 2.17 2.33 -0.33 0.00 0.50 0.00 0.33 0.00 1.00 0.00 4.67 -2.50 0.00 -1.33 0.00 0.27 0.27
3.67 0.00 0.50 2.50 3.33 -2.33 2.83 0.17 -0.50 0.00 0.83 -1.33 -0.83 1.67 0.00 1.67 1.17 -0.33 3.50 1.50 0.00 -0.17 -2.67 0.00 -2.00 0.00 0.27 0.27
0.83 0.00 -1.83 5.67 4.00 -3.50 1.67 3.83 -1.17 0.00 1.17 -2.00 -1.83 2.83 0.00 0.67 3.00 0.83 0.33 0.50 0.00 -1.17 -3.83 0.00 -1.17 0.00 0.27 0.27
1.83 0.00 0.17 1.50 1.50 -2.83 1.83 1.00 -1.00 0.00 1.17 -1.33 -0.83 1.17 0.00 3.67 2.83 1.33 3.00 0.83 0.00 -0.33 -1.67 0.00 -3.00 0.00 0.27 0.27
0.17 0.00 -0.67 -1.50 -1.17 3.33 -1.00 -1.33 5.67 0.00 -1.17 5.17 4.00 -1.67 0.00 -0.67 -1.00 -1.67 -1.00 0.50 0.00 5.67 -1.33 0.00 0.50 0.00 0.27 0.27
0.50 0.00 -3.00 2.67 3.50 -3.00 0.50 1.00 -1.00 0.00 5.50 -1.50 0.33 2.17 0.00 0.50 2.33 2.67 1.00 1.00 0.00 -1.00 -1.50 0.00 -2.83 0.00 0.27 0.27
1.67 0.00 -0.33 0.67 0.83 -0.67 2.67 -1.00 0.83 0.00 0.50 1.00 2.00 0.50 0.00 0.67 0.17 -0.33 1.00 3.17 0.00 1.67 -3.17 0.00 -1.67 0.00 0.27 0.27
-1.50 0.00 0.17 -3.33 -2.33 6.67 -2.83 0.00 2.50 0.00 -2.50 5.00 2.67 -1.67 0.00 -2.83 -2.50 -2.50 -1.83 -1.17 0.00 1.50 4.67 0.00 5.17 0.00 0.27 0.27
0.17 0.00 -3.33 0.67 1.00 -0.33 -0.67 0.83 0.50 0.00 2.67 1.83 2.33 0.67 0.00 0.17 3.00 1.33 -0.50 0.00 0.00 0.67 0.17 0.00 -1.50 0.00 0.27 0.27
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-0.33 0.00 -0.17 -0.67 -0.50 3.33 -1.17 1.00 1.00 0.00 -0.83 2.33 1.33 1.67 0.00 -1.83 -0.50 -1.50 -0.83 -0.33 0.00 0.67 2.17 0.00 2.83 0.00 0.27 0.27
0.50 0.00 -1.00 -0.50 -0.17 1.50 -0.17 -0.50 1.67 0.00 -0.17 2.33 2.00 -0.33 0.00 0.00 -0.33 -0.83 -0.17 2.33 0.00 1.67 -0.17 0.00 0.00 0.00 0.27 0.27
0.33 0.00 0.67 -0.67 -0.67 1.33 -0.17 -1.00 4.33 0.00 -0.67 2.67 2.00 -1.00 0.00 -0.17 -0.83 -1.00 -0.33 0.67 0.00 4.33 -2.17 0.00 0.00 0.00 0.27 0.27
0.83 0.00 0.17 0.17 0.17 -1.00 0.50 0.33 -0.33 0.00 0.17 -0.50 -0.33 0.00 0.00 2.50 0.50 0.50 0.67 0.50 0.00 0.17 -1.33 0.00 -1.33 0.00 0.27 0.27
0.67 0.00 1.00 0.33 0.33 -0.50 1.00 -0.33 -0.17 0.00 0.33 -0.67 -0.50 0.50 0.00 0.67 -0.17 0.17 2.50 0.50 0.00 -0.17 0.50 0.00 -0.67 0.00 0.27 0.27
-0.50 0.00 -0.50 0.00 0.00 -0.83 -0.50 0.83 -0.50 0.00 1.33 -0.67 0.33 0.17 0.00 0.50 0.67 2.50 0.17 -0.17 0.00 -0.50 2.17 0.00 -1.00 0.00 0.27 0.27
0.33 0.00 -0.50 1.00 0.83 -0.83 0.67 0.83 -0.50 0.00 0.67 -0.67 -0.50 2.50 0.00 0.00 0.67 0.17 0.50 0.33 0.00 -0.50 -0.50 0.00 -0.17 0.00 0.27 0.27
-0.83 0.00 -0.17 -1.67 -1.00 2.50 -1.00 -0.17 1.00 0.00 -1.00 2.00 0.83 -0.83 0.00 -1.00 -1.33 -0.83 -0.50 -0.50 0.00 0.33 2.00 0.00 2.17 0.00 0.27 0.27
2.50 0.00 0.50 0.50 0.50 -0.83 1.00 -0.17 0.00 0.00 0.00 -0.17 0.00 0.33 0.00 0.83 0.33 -0.50 0.67 0.67 0.00 0.33 -1.33 0.00 -0.50 0.00 0.27 0.27
2.50 0.00 0.50 0.50 0.50 -0.83 1.00 -0.17 0.00 0.00 0.00 -0.17 0.00 0.33 0.00 0.83 0.33 -0.50 0.67 0.67 0.00 0.33 -1.33 0.00 -0.50 0.00 0.27 0.27
-0.17 0.00 -1.33 -0.83 -0.50 2.00 -0.83 -0.33 1.33 0.00 -0.50 2.50 2.00 -0.67 0.00 -0.50 -0.17 -0.67 -0.67 -0.17 0.00 1.33 0.83 0.00 0.50 0.00 0.27 0.27
-0.50 0.00 -0.50 0.00 0.00 -0.83 -0.50 0.83 -0.50 0.00 1.33 -0.67 0.33 0.17 0.00 0.50 0.67 2.50 0.17 -0.17 0.00 -0.50 2.17 0.00 -1.00 0.00 0.27 0.27
-0.17 0.00 -1.33 -0.83 -0.50 2.00 -0.83 -0.33 1.33 0.00 -0.50 2.50 2.00 -0.67 0.00 -0.50 -0.17 -0.67 -0.67 -0.17 0.00 1.33 0.83 0.00 0.50 0.00 0.27 0.27
0.50 0.00 -0.83 2.50 1.67 -1.67 1.00 0.67 -0.33 0.00 0.50 -0.83 -0.67 1.00 0.00 0.17 1.00 0.00 0.33 0.33 0.00 -0.33 -1.83 0.00 -0.83 0.00 0.27 0.27
-0.50 0.00 -0.50 0.00 0.00 -0.83 -0.50 0.83 -0.50 0.00 1.33 -0.67 0.33 0.17 0.00 0.50 0.67 2.50 0.17 -0.17 0.00 -0.50 2.17 0.00 -1.00 0.00 0.27 0.27
0.50 0.00 -1.00 1.67 2.50 -1.00 0.83 0.67 -0.33 0.00 0.50 -0.50 -0.33 0.83 0.00 0.17 1.00 0.00 0.33 0.33 0.00 -0.33 -1.83 0.00 -0.83 0.00 0.27 0.27
-0.50 0.00 1.67 -0.83 -0.83 2.17 -1.00 0.50 0.17 0.00 -1.00 0.50 -0.17 -0.17 0.00 -1.33 -1.00 -1.00 -0.67 -0.50 0.00 -0.17 1.83 0.00 2.50 0.00 0.27 0.27
-0.83 0.00 -0.17 -1.67 -1.00 2.50 -1.00 -0.17 1.00 0.00 -1.00 2.00 0.83 -0.83 0.00 -1.00 -1.33 -0.83 -0.50 -0.50 0.00 0.33 2.00 0.00 2.17 0.00 0.27 0.27
0.50 0.00 -0.83 2.50 1.67 -1.67 1.00 0.67 -0.33 0.00 0.50 -0.83 -0.67 1.00 0.00 0.17 1.00 0.00 0.33 0.33 0.00 -0.33 -1.83 0.00 -0.83 0.00 0.27 0.27




5.0 DATA FILES

LIBGEN require a residue substitution matrix for the generation of certain types of profile.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-dafinpath]         dirlist    This option specifies the location of DAF
                                  files (domain alignment files) (input). A
                                  'domain alignment file' contains a sequence
                                  alignment of domains belonging to the same
                                  SCOP or CATH family. The file is in clustal
                                  format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
   -matrixfile         matrixf    This option specifies the residue
                                  substitution matrix. Epprofile for Gribskov
                                  profiles or EBLOSUM62 otherwise.
   -mode               menu       This option specifies the mode of LIBGEN
                                  operation. LIBGEN generates one of six types
                                  of profile for each alignment. Supported
                                  profiles include simple frequency matrices,
                                  Gribskov profiles, Hennikoff profiles,
                                  hidden Markov models (HMMER package), hidden
                                  Markov models (SAM-T2K package) and
                                  position-specific scoring matrices.
*  -threshold          integer    This option specifies the threshold
                                  reporting percentage. The threshold
                                  reporting percentage is used in the
                                  construction of the simple frequency matrix.
*  -gapopen            float      This option specifies the gap insertion
                                  penalty. The gap insertion penalty is the
                                  score taken away when a gap is created. The
                                  best value depends on the choice of
                                  comparison matrix. The default value assumes
                                  you are using the EBLOSUM62 matrix for
                                  protein sequences, and the EDNAFULL matrix
                                  for nucleotide sequences.
*  -gapextend          float      This option specifies the gap extension
                                  penalty. The gap extension, penalty is added
                                  to the standard gap penalty for each base
                                  or residue in the gap. This is how long gaps
                                  are penalized. Usually you will expect a
                                  few long gaps rather than many short gaps,
                                  so the gap extension penalty should be lower
                                  than the gap penalty. An exception is where
                                  one or both sequences are single reads with
                                  possible sequencing errors in which case
                                  you would expect many single base gaps. You
                                  can get this result by setting the gap open
                                  penalty to zero (or very low) and using the
                                  gap extension penalty to control gap
                                  scoring.
  [-outdir]            outdir     This option specifies the location of
                                  discriminator files (output). The
                                  discriminator files contain one of the
                                  supported profiles, including simple
                                  frequency matrices, Gribskov profiles,
                                  Hennikoff profiles, hidden Markov models
                                  (HMMER package), hidden Markov models
                                  (SAM-T2K package) and position-specific
                                  scoring matrices.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


Standard (Mandatory) qualifiers Allowed values Default
[-dafinpath]
(Parameter 1)
This option specifies the location of DAF files (domain alignment files) (input). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Directory with files ./
-matrixfile This option specifies the residue substitution matrix. Epprofile for Gribskov profiles or EBLOSUM62 otherwise. Comparison matrix file in EMBOSS data path Epprofile for Gribskov type, or EBLOSUM62
-mode This option specifies the mode of LIBGEN operation. LIBGEN generates one of six types of profile for each alignment. Supported profiles include simple frequency matrices, Gribskov profiles, Hennikoff profiles, hidden Markov models (HMMER package), hidden Markov models (SAM-T2K package) and position-specific scoring matrices.
1 (Simple frequency matrix)
2 (Gribskov profile)
3 (Henikoff profile)
4 (Hidden Markov model (HMMER))
5 (Hidden Markov model (SAM-T2K))
6 (Position-specific scoring matrix)
1
-threshold This option specifies the threshold reporting percentage. The threshold reporting percentage is used in the construction of the simple frequency matrix. Integer from 1 to 100 75
-gapopen This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Any numeric value 3.0
-gapextend This option specifies the gap extension penalty. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Any numeric value 0.3
[-outdir]
(Parameter 2)
This option specifies the location of discriminator files (output). The discriminator files contain one of the supported profiles, including simple frequency matrices, Gribskov profiles, Hennikoff profiles, hidden Markov models (HMMER package), hidden Markov models (SAM-T2K package) and position-specific scoring matrices. Output directory ./
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

6.2 EXAMPLE SESSION

An example of interactive use of LIBGEN is shown below. Here is a sample session with libgen


% libgen 
Generates various types of discriminating elements for each alignment in a
directory.
Location of DAF files (domain alignment files) (input). [./]: structure
Residue substitution matrix. [EBLOSUM62]: EBLOSUM62
Discrimininator type
         1 : Simple frequency matrix
         2 : Gribskov profile
         3 : Henikoff profile
         4 : Hidden Markov model (HMMER)
         5 : Hidden Markov model (SAM-T2K)
         6 : Position-specific scoring matrix
Select type. [1]: 2
Location of discriminator files (output). [./]: 

Go to the output files for this example

Domain alignment files of file extension .salign (specified in ACD) were read from /test_data. A Gribskov profile was generated and written to /test_data/libgen. The EBLOSUM62 residue substitution matrix was used.


7.0 KNOWN BUGS & WARNINGS

Be careful to select the appropriate matrix which is not necessarily the suggested default matrix. You should normally pick Epprofile for Gribskov profiles or EBLOSUM62 otherwise.

A matrix is prompted for but not actually required for HMM generation: this behaviour will be fixed in a future version.


8.0 NOTES

LIBGEN requires a working version of HMMER and SAM-T2K installed on the same machine if the corresponding modes are selected.

When running libgen at the HGMP it is essential that the command 'use hmmer' (which runs the script /packages/menu/USE/hmmer) is given before it is run.

When running libgen at the HGMP it is essential that the command 'use samt2k' (which runs the script /packages/menu/USE/samt2k) is given before it is run.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
Domain alignment file DAF format (CLUSTAL-like format with domain classification information). Contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is annotated with domain family classification information. DOMAINALIGN (structure-based sequence alignment of domains of known structure). DOMAINALIGN alignments can be extended with sequence relatives (of unknown structure) to the family in question by using SEQALIGN.
Hidden Markov models A file containing a hidden Markov model. Can be generated for SCOP or CATH families by using LIBGEN which uses the HMMER & SAM-T2K packages. N.A.
Simple frequency matrices, Gribskov profiles, Hennikoff profiles & position-specific scoring matrices A file containing a simple frequency matrix, Gribskov profile, Hennikoff profile or position-specific scoring matrix. Can be generated for SCOP or CATH families by using LIBGEN, which uses the BLAST package. N.A.
None


9.0 DESCRIPTION

LIBGEN provides a convenient means to generate various types of profile and hidden Markov models from alignments for protein families. The profiles are descriptive of the family and can be used to identify sequence relatives of the family.


10.0 ALGORITHM

Functions from the emboss application prophecy have been incorporated.


11.0 RELATED APPLICATIONS

See also

Program nameDescription
contactcountCounts specific versus non-specific contacts in a directory of cleaned protein chain contact files
contactsReads CCF files (clean coordinate files) and writes CON files (contact files) of intra-chain residue-residue contact data
domainalignGenerates DAF files (domain alignment files) of structure-based sequence alignments for nodes in a DCF file (domain classification file)
domainrepReorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first
domainresoRemoves low resolution domains from a DCF file (domain classification file)
interfaceReads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data
psiphiCalculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file
roconReads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a 'hits file' for the hits, which are classified and rank-ordered on the basis of score
rocplotProvides interpretation and graphical display of the performance of discriminating elements (e.g. profiles for protein families). rocplot reads file(s) of hits from discriminator-database search(es), performs ROC analysis on the hits, and writes graphs illustrating the diagnostic performance of the discriminating elements
seqalignReads a DAF file (domain alignment file) and a DHF file (domain hits file) and writes a DAF file extended with the hits
seqfraggleRemoves fragments from DHF files (domain hits files) or other files of sequences
seqsearchGenerate database hits (sequences) for nodes in a DCF file (domain classification file) by using PSI-BLAST
seqsortReads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification
seqwordsGenerates DHF files (domain hits files) of database hits (sequences) for nodes in a DCF file (domain classification file) by keyword search of UniProt
siggenGenerates a sparse protein signature from an alignment and residue contact data
sigscanGenerates a DHF file (domain hits file) of hits (sequences) from scanning a signature against a sequence database



12.0 DIAGNOSTIC ERROR MESSAGES

None.


13.0 AUTHORS

Jon Ison (jison@rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Based on the original profgen and hmmgen applications written by

Ranjeeva Ranasinghe (rranasin@rfcgr.mrc.ac.uk)


14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

14.1 Other useful references