est2genome - Align EST sequences to genomic DNA sequence

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       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).

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EMBOSS 6.4.0                                       05/11/2012                                     EST2GENOME(1e)

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).

       est2genome - Align EST sequences to genomic DNA sequence

Inputsection-estsequenceseqall-genomesequencesequenceAdditionalsection-matchinteger
           Default value: 1

       -mismatchinteger
           Default value: 1

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

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

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

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

   Advancedsection-reverseboolean
           Reverse the orientation of the EST sequence

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

       -modelist
           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

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

       -spacefloat
           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

       -shuffleinteger-seedinteger
           Default value: 20825

   Outputsection-outfileoutfile-alignboolean
           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).

       -widthinteger
           Default value: 50

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

est2genome-estsequenceseqall-genomesequencesequence [-matchinteger] [-mismatchinteger]
                  [-gappenaltyinteger] [-intronpenaltyinteger] [-splicepenaltyinteger] [-minscoreinteger]
                  -reverseboolean-usespliceboolean-modelist-bestboolean-spacefloat-shuffleinteger-seedinteger-outfileoutfile-alignboolean-widthintegerest2genome-help