est2genome - Align EST sequences to genomic DNA sequence
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
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).
-estsequence seqall
-genomesequence sequence
-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
-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
-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 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).
est2genome is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
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.