[EMBOSS] fuzzpro oddity

Andres Pinzon andrespinzon at gmail.com
Fri Mar 13 15:36:17 UTC 2009

Hi Steve,
just in case you have to change J for X in several fasta files,
several times, this bash script does the job:

find -type f -name '*.fasta' -print0 | xargs --null perl -pi -e 's/J/X/'

Hope it helps,


On Fri, Mar 13, 2009 at 11:26 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
> Steve Taylor wrote:
>> Thanks Peter.
>> Nice detective work. I wonder if anybody in NCBI/RefSeq is reading this?
>> This is where the source is from...I wonder how blast indexing handles not
>> having a > for example?
> There was a '>' ... my mailer uses it for quoting so it got converted to
> '&gt' but the file was OK. It was only the 'J' in the sequnece that broke
> things.
> Peter
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Andrés Pinzón
Bioinformatics Center, Colombia EMBnet node
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768

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