[EMBOSS] Needle

Sean.Maceachern at dpi.vic.gov.au Sean.Maceachern at dpi.vic.gov.au
Thu Oct 2 07:04:23 UTC 2003


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.

Thank you

Sean MacEachern

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