est2genome1e
Align est sequences to genomic dna sequence
Usage
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
Overview
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.
-usesplice since Debian 6.0 (Squeeze).
-splice until Debian 5.0 (Lenny).