[EMBOSS] Needle

David Martin d.m.a.martin at dundee.ac.uk
Thu Oct 2 08:17:42 UTC 2003

On 2/10/03 8:04 am, "Sean.Maceachern at dpi.vic.gov.au"
<Sean.Maceachern at dpi.vic.gov.au> wrote:

> Hello,
> I am a novice at all things computer and i was hoping that someone might be
> able to give me some advice. I am working with two lynux machines with
> different versions of Emboss on them. I have noticed that in the most
> recent version of emboss the needle outputs have changed. I need to work
> with the 'old' fasta output that used to have trailing gaps/indels as white
> space and internal gaps/indels as periods '.' . I have found that the most
> recent version of emboss has changed the output format so now the fasta
> format looks more like a clustal output with gaps/indels represented as a '
> -' whether thay are terminal or inserted within the sequence. I was hoping
> someone could point me towards a similar output for the new version of
> emboss or if it is not too much trouble to make a new format based on the
> fasta format from an older version of needle.

You will find that you can set the alignment format output by programs like
needle using a command line flag. the EMBOSS website has full details of
this at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignFormats.html



> Thank you
> Sean MacEachern

David Martin PhD
Bioinformatics Scientific Officer
Post-Genomics and Molecular Interactions Centre
University of Dundee

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