SYNOPSIS

needle -asequence sequence -bsequence seqall [-datafile matrixf] -gapopen float -gapextend float [-endweight boolean] [-endopen float] [-endextend float] -brief boolean -outfile align

needle -help

DESCRIPTION

needle

OPTIONS

Input section

-asequence sequence

-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. This is how long end gaps are penalized. Default value: @($(acdprotein)? 0.5 : 0.5 )

Output section

-brief boolean

Brief identity and similarity Default value: Y

-outfile align

AUTHOR

Debian Med Packaging Team <[email protected]>

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.