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.TH MAKEMAT 1 2004-06-25 NCBI "NCBI Tools User's Manual"
.SH NAME
makemat \- convert binary profiles into portable ASCII form
.SH SYNOPSIS
.B makemat
[\|\fB\-\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-H\fP\|]
[\|\fB\-P\fP\ \fIfilename\fP\|]
[\|\fB\-S\fP\ \fIX\fP\|]
[\|\fB\-U\fP\ \fIstr\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-z\fP\ \fIN\fP\|]
.SH DESCRIPTION
\fBmakemat\fP converts a collection of binary profiles, created by the
\fB\-C\fP option of PSI-BLAST, into portable ASCII form.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-E\fP\ \fIN\fP
Cost to extend a gap (default = \fB1\fP)
.TP
\fB\-G\fP\ \fIN\fP
Cost to open a gap (default = \fB11\fP)
.TP
\fB\-H\fP
Print help; overrides all other arguments
.TP
\fB\-P\fP\ \fIfilename\fP
Database name for profile database (default = \fBstdin\fP)
.TP
\fB\-S\fP\ \fIX\fP
Scaling factor for matrix outputs to avoid round-off problems (default
= \fB100\fP)
.TP
\fB\-U\fP\ \fIstr\fP
Underlying Matrix (default = \fBBLOSUM62\fP)
.TP
\fB\-d\fP\ \fIstr\fP
Underlying sequence database used to make profiles (default = \fBnr\fP)
.TP
\fB\-z\fP\ \fIN\fP
Effective length of the profile database (0 for length of \fB\-d\fP option)
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR blast (1),
.BR copymat (1),
impala.html
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