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
- Default value: 1
- Default value: 1
- Cost for deleting a single base in either sequence, excluding introns Default value: 2
- Cost for an intron, independent of length. Default value: 40
- Cost for an intron, independent of length and starting/ending on donor-acceptor sites Default value: 20
- Exclude alignments with scores below this threshold score. Default value: 30
- Reverse the orientation of the EST sequence
- Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then set this to be false. Default value: Y
- 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
- You can print out all comparisons instead of just the best one by setting this to be false. Default value: Y
- 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
- Default value: 20825
- 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).
- 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).
Debian Med Packaging Team <[email protected]>
- 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.