NAME

       est2genome - Align EST sequences to genomic DNA sequence

SYNOPSIS

       est2genome -estsequence seqall -genomesequence sequence [-match integer]
                  [-mismatch integer] [-gappenalty integer] [-intronpenalty integer]
                  [-splicepenalty integer] [-minscore integer] -reverse boolean
                  -usesplice boolean -mode list -best boolean -space float -shuffle integer
                  -seed integer -outfile outfile -align boolean -width integer

       est2genome -help

DESCRIPTION

       est2genome is a command line program from EMBOSS (“the European Molecular Biology Open
       Software Suite”). It is part of the "Alignment:Global" command group(s).

OPTIONS

   Input section
       -estsequence seqall

       -genomesequence sequence

   Additional section
       -match integer
           Default value: 1

       -mismatch integer
           Default value: 1

       -gappenalty integer
           Cost for deleting a single base in either sequence, excluding introns Default value: 2

       -intronpenalty integer
           Cost for an intron, independent of length. Default value: 40

       -splicepenalty integer
           Cost for an intron, independent of length and starting/ending on donor-acceptor sites
           Default value: 20

       -minscore integer
           Exclude alignments with scores below this threshold score. Default value: 30

   Advanced section
       -reverse boolean
           Reverse the orientation of the EST sequence

       -usesplice boolean
           Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then
           set this to be false. Default value: Y

       -mode list
           This determines the comparison mode. The default value is 'both', 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 'forward', when just the forward strand is
           searched, and 'reverse', ditto for the reverse strand. Default value: both

       -best boolean
           You can print out all comparisons instead of just the best one by setting this to be
           false. Default value: Y

       -space float
           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's physical RAM) Default
           value: 10.0

       -shuffle integer

       -seed integer
           Default value: 20825

   Output section
       -outfile outfile

       -align boolean
           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).

       -width integer
           Default value: 50

BUGS

       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).

SEE ALSO

       est2genome is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       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.