This is the command needlee 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
needle - Needleman-Wunsch global alignment of two sequences
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 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 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
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