Provided by: emboss_6.6.0+dfsg-7_amd64
needleall - Many-to-many pairwise alignments of two sequence sets
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
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).
Input section -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
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).
needleall is fully documented via the tfm(1) system.
Debian Med Packaging Team <email@example.com> 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.