est2genomee - Online in the Cloud

PROGRAM:

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

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