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'\" t
.\" Title: EST2GENOME
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\" Date: 05/11/2012
.\" Manual: EMBOSS Manual for Debian
.\" Source: EMBOSS 6.4.0
.\" Language: English
.\"
.TH "EST2GENOME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.\" disable hyphenation
.nh
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.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
est2genome \- Align EST sequences to genomic DNA sequence
.SH "SYNOPSIS"
.HP \w'\fBest2genome\fR\ 'u
\fBest2genome\fR \fB\-estsequence\ \fR\fB\fIseqall\fR\fR \fB\-genomesequence\ \fR\fB\fIsequence\fR\fR [\fB\-match\ \fR\fB\fIinteger\fR\fR] [\fB\-mismatch\ \fR\fB\fIinteger\fR\fR] [\fB\-gappenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-intronpenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-splicepenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIinteger\fR\fR] \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-usesplice\ \fR\fB\fIboolean\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-best\ \fR\fB\fIboolean\fR\fR \fB\-space\ \fR\fB\fIfloat\fR\fR \fB\-shuffle\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-align\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR
.HP \w'\fBest2genome\fR\ 'u
\fBest2genome\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBest2genome\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-estsequence\fR \fIseqall\fR
.RS 4
.RE
.PP
\fB\-genomesequence\fR \fIsequence\fR
.RS 4
.RE
.SS "Additional section"
.PP
\fB\-match\fR \fIinteger\fR
.RS 4
Default value: 1
.RE
.PP
\fB\-mismatch\fR \fIinteger\fR
.RS 4
Default value: 1
.RE
.PP
\fB\-gappenalty\fR \fIinteger\fR
.RS 4
Cost for deleting a single base in either sequence, excluding introns Default value: 2
.RE
.PP
\fB\-intronpenalty\fR \fIinteger\fR
.RS 4
Cost for an intron, independent of length\&. Default value: 40
.RE
.PP
\fB\-splicepenalty\fR \fIinteger\fR
.RS 4
Cost for an intron, independent of length and starting/ending on donor\-acceptor sites Default value: 20
.RE
.PP
\fB\-minscore\fR \fIinteger\fR
.RS 4
Exclude alignments with scores below this threshold score\&. Default value: 30
.RE
.SS "Advanced section"
.PP
\fB\-reverse\fR \fIboolean\fR
.RS 4
Reverse the orientation of the EST sequence
.RE
.PP
\fB\-usesplice\fR \fIboolean\fR
.RS 4
Use donor and acceptor splice sites\&. If you want to ignore donor\-acceptor sites then set this to be false\&. Default value: Y
.RE
.PP
\fB\-mode\fR \fIlist\fR
.RS 4
This determines the comparison mode\&. The default value is \*(Aqboth\*(Aq, in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparison redone assuming a reversed (CT/AC) gene splicing direction\&. The other allowed modes are \*(Aqforward\*(Aq, when just the forward strand is searched, and \*(Aqreverse\*(Aq, ditto for the reverse strand\&. Default value: both
.RE
.PP
\fB\-best\fR \fIboolean\fR
.RS 4
You can print out all comparisons instead of just the best one by setting this to be false\&. Default value: Y
.RE
.PP
\fB\-space\fR \fIfloat\fR
.RS 4
For linear\-space recursion\&. If product of sequence lengths divided by 4 exceeds this then a divide\-and\-conquer strategy is used to control the memory requirements\&. In this way very long sequences can be aligned\&. If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine\*(Aqs physical RAM) Default value: 10\&.0
.RE
.PP
\fB\-shuffle\fR \fIinteger\fR
.RS 4
.RE
.PP
\fB\-seed\fR \fIinteger\fR
.RS 4
Default value: 20825
.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
.RE
.PP
\fB\-align\fR \fIboolean\fR
.RS 4
Show the alignment\&. The alignment includes the first and last 5 bases of each intron, together with the intron width\&. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown)\&.
.RE
.PP
\fB\-width\fR \fIinteger\fR
.RS 4
Default value: 50
.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
.SH "SEE ALSO"
.PP
est2genome is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
.sp
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