FOLDALIGN

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makematrix


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NAME

makefamatrix -Generates scoring matrix for FOLDALIGN  

SYNOPSIS

makefamatrix [-lsize number] [-bpelon number] [-inbp_mat file] [-ibp_mat file] [-enbp_mat file] [-ebp_mat file]  

OPTIONS

makefamatrix accepts the following option.

-lsize number

Minimum allowed loop size. Default is 3.

-bpelon number

Base-pair elongation factor. Default is 1.

-inbp_mat file

Matrix file for gap initiation cost and no base-pair cost.

-ibp_mat file

Matrix file for gap initiation cost with base-pair cost.

-enbp_mat file

Matrix file for gap elongation cost and no base-pair cost.

-ebp_mat file

Matrix file for gap elongation cost with base-pair cost.

REQUIRED EXECUTABLES

makefamatrix requires the existence of

*

$FOLDALIGN_DIR/bin/genmatrix

EXAMPLES

Examples of the four types of matrices needed can be found in $FOLDALIGN_DIR/lib/*.mat. An on execution:

makefamatrix -lsize 4 -inbp_mat inbp.mat -ibp_mat ibp.mat -enbp_mat enbp.mat -ebp_mat ebp.mat

AUTHORS

Laurie J. Heyer and Jan Gorodkin
(laheyer@davidson.edu and gorodkin@bioinf.au.dk)

REFERENCES

For any use of FOLDALIGN programs please cite:

J. Gorodkin, L. J. Heyer and G. D. Stormo. Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Research, 25:18, 3724-3732, 1997.

J. Gorodkin, L. J. Heyer and G. D. Stormo. Finding Common Sequence and Structure Motifs in a set of RNA sequences. Proceedings ISMB-97, pp. 120-123, 1997.

CONTACT

If you have questions, bug reports, complaints, comments, requests, email foldalign@bioinf.au.dk.

SEE ALSO

FOLDALIGN, fa2col, sortfalign, prefilter, mainfilter, makefamatrix, genmatrix

Index

NAME

SYNOPSIS

OPTIONS

REQUIRED EXECUTABLES

EXAMPLES

AUTHORS

REFERENCES

CONTACT

SEE ALSO

Comments, questions, etc., email foldalign@bioinf.au.dk