mt-anno.1

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.TH MT-ANNO 1 "JANUARY 2014" Applications "User Manuals"
.SH NAME
mt-anno \- annotate a
.IR human (!)
mitochondrion

.SH SYNOPSIS
.B mt-anno 
<
.I junk.fa
> 
.I crap.txt

.SH DESCRIPTION
.B mt-anno
reads a set of
.IR human (!)
mitochondrial sequences in fasta format from stdin and for each of them
writes a Genbank formatted annotation and the set of coded protein
sequences in fasta format to stdout.

The annotation is built in and applied blindly.  This is a 
.IR "very stupid" ", " "very useless" " and " "very wasteful"
thing to do, but biologists have been asking for it repeatedly.  
.B DO NOT USE
this tool if you like to think of yourself as a scientist!

.SH OPTIONS

.B mt-anno
comes without options and is not customizable.  If you think any options
or any further documentation might be useful, you are confused.
Actually, if you want to use it at all, you are confused.

.SH BUGS

All 
.B mt-anno
does is take the "official" annotation of rCRS and translate its
coordinates.  If after translation the annotation doesn't make sense
anymore, there is no warning.  If translated proteins lost their start
codon or gained a stop codon, there is no warning.  If there is a
frame shift mutation, there is no warning.  Arguable, the whole idea of
.B mt-anno
is one big bug, but it's considered unfixable.

.SH AUTHOR
Udo Stenzel <udo_stenzel@eva.mpg.de>

.SH "SEE ALSO"
.BR biohazard (7), fasta (5)