NEEDLEALL(1e) | EMBOSS Manual for Debian | NEEDLEALL(1e) |
NAME¶
needleall - Many-to-many pairwise alignments of two sequence setsSYNOPSIS¶
needleall
-asequence seqset
-bsequence seqall [
-datafile matrixf]
-gapopen float
-gapextend float [
-endweight boolean] [
-endopen float]
[-endextend float] [
-minscore float]
-brief boolean
-outfile align [
-errorfile outfile]
needleall
-help
DESCRIPTION¶
needleall 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¶
-asequence seqset -bsequence seqall -datafile matrixfThis is the scoring matrix file used when
comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or
the file 'EDNAFULL' (for nucleic sequences). These files are found in the
'data' directory of the EMBOSS installation.
Required section¶
-gapopen floatThe gap open penalty is the score taken away
when a gap is created. The best value depends on the choice of comparison
matrix. The default value assumes you are using the EBLOSUM62 matrix for
protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default
value: @($(acdprotein)? 10.0 : 10.0 )
-gapextend float
The gap extension, penalty is added to the
standard gap penalty for each base or residue in the gap. This is how long
gaps are penalized. Usually you will expect a few long gaps rather than many
short gaps, so the gap extension penalty should be lower than the gap penalty.
An exception is where one or both sequences are single reads with possible
sequencing errors in which case you would expect many single base gaps. You
can get this result by setting the gap open penalty to zero (or very low) and
using the gap extension penalty to control gap scoring. Default value:
@($(acdprotein)? 0.5 : 0.5 )
Additional section¶
-endweight booleanDefault value: N
-endopen float
The end gap open penalty is the score taken
away when an end gap is created. The best value depends on the choice of
comparison matrix. The default value assumes you are using the EBLOSUM62
matrix for protein sequences, and the EDNAFULL matrix for nucleotide
sequences. Default value: @($(acdprotein)? 10.0 : 10.0 )
-endextend float
The end gap extension, penalty is added to the
end gap penalty for each base or residue in the end gap. Default value:
@($(acdprotein)? 0.5 : 0.5 )
-minscore float
Minimum alignment score to report an
alignment.
Output section¶
-brief booleanBrief identity and similarity Default value:
Y
-outfile align
-errorfile outfile
Error file to be written to Default value:
needleall.error
BUGS¶
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).SEE ALSO¶
needleall is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this
manual page.
COPYRIGHT¶
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.05/11/2012 | EMBOSS 6.4.0 |