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est2genomee - Online in the Cloud

Run est2genomee in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command est2genomee that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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