'\" t .\" Title: EST2GENOME .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" 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" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * 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