NAME¶
needleall - Many-to-many pairwise alignments of two sequence
sets
SYNOPSIS¶
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¶
-asequence seqset
-bsequence seqall
-datafile matrixf
This 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 float
The 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 boolean
Default 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 boolean
Brief identity and similarity Default value: Y
-outfile align
-errorfile outfile
Error file to be written to Default value:
needleall.error
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.
