This is the command needlealle that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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
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