.TH "xnu" 1 "February 18, 1992"
\" This is the on-line manual page for xnu.
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\" The operation of the 'man' command can be simulated with the command:
\"		nroff -man xnu.1 | ul | more
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.UC 4
.SH NAME
xnu \- exclude non-unique
.SH SYNOPSIS
.LP
.B xnu
fasta-protein-sequences-file [options]
.br
[-n search-width] [-p probability-cut] [-s score-cut]
.br
[-60] [-120] [-250] 
.br
[-.] [-x] [-o] [-a] [-d] [-r] [-v]
.sp
.br
.SH DESCRIPTION
.LP
Functionally,
.I
xnu
will read a file containing FASTA format protein sequences.
It will search each sequence for statistically significant
tandem repeats.
.LP
The motivation for this program is to filter sequences or databases
of sequences to eliminate short period internal repeats which
would confound the scoring of sequence similarity searches.
.LP
For
.I
xnu
the PAM120 matrix is used for scoring similarities,
internal repeats with a period of less then or equal to 4 are
eliminated, and the expectation cutoff for elimination is 0.01.
Repeat sequences will be replaced by a space holding character
in the output sequence.  By default both of the segments in the
alignment defining the internal repeat will be replaced by
the space holder 'X'.
.LP

.SH OPTIONS
.LP
.B \-n 10
Set the width to search for internal repeats.
The value 0 will search for internal repeats of any period.
.LP
.B \-p 0.01
Set the probability cutoff for accepting an internal repeat as
significant.
.LP
.B \-s
Set the score cutoff for accepting an internal repeat as
significant.  By default this is calculated from the probability
cutoff, sequence length, and scoring matrix using the standard
Dayhoff amino acid frequencies.
.LP
.B \-60
Use PAM60 scoring matrix. (xnu only)
.LP
.B \-120
Use PAM120 scoring matrix. (xnu only)
.LP
.B \-250
Use PAM250 scoring matrix. (xnu only)
.LP
.B \-.
Print a '.' as the space holder in place of eliminated sequences
in the output.
.LP
.B \-x
Print an 'X' as the space holder in place of eliminated sequences
in the output.
.LP
.B \-o
Print the sequence in lowercase  as the space holder in place of 
eliminated sequences in the output.
.LP
.B \-a
Eliminate only the ascending half of an alignment.
.LP
.B \-d
Eliminate only the descending half of an alignment.
.LP
.B \-r
Reverse the output and print the repeats while eliminating
the unique portion of the sequence.
.LP
.B \-v
Turns the verbose flag on. Default is off.
Verbose output is sent to stdout.

.SH EXAMPLE
Assuming a file named 'seq' contains the following:
.nf

>Sample sequence with internal repeats
ACDEFGHIKLMNPQRQRQRQRQRQRQRQRQRSTVWY


	xnu seq

will print the sequence with the repeats eliminated:

>Sample sequence with internal repeats
ACDEFGHIKLMNPXXXXXXXXXXXXXXXXXXSTVWY

	xnu seq -r

will print the repetitive part of the sequence:

>Sample sequence with internal repeats
XXXXXXXXXXXXXQRQRQRQRQRQRQRQRQRXXXXX

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\" When ever possible, pointers to related commands should be given.
.SH SEE ALSO
.LP
.I
fasta, blast, seg
\" This section can be real useful.
.SH BUGS
Feature: Only a fixed set of scoring systems is allowed.
.LP
Feature: The algorithm is a simple search.  For long sequences and large
search widths, it can be slow.

.SH REFERENCES
.nf
Jean Michel Claverie & David J. States (1993)
Information Enhancement Methods for Large Scale Sequence Analysis,
Computers and Chemistry 17: 191-201.

Jean Michel Claverie (1993)
Large Scale Sequence Analysis, Chapter 36 in
"Automated DNA sequencing and analysis techniques"
(J.C. Venter, ed), Academic Press

National Center for Biotechnology Information
National Library of Medicine
8600 Rockville Pike,  38A 8S806
Bethesda, MD  20894
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