# [EMBOSS] Jemboss/EMBOSS can't find the external clustalw binary

Nigel Binns n.binns at ed.ac.uk
Wed Aug 11 13:31:09 UTC 2010

  Hi All,

Please can anyone tell me why my installation of Jemboss (EMBOSS v6.3.1
patch v1-4) can't find the external clustal binary and how to correct
this. When I run a multiple sequence alignment using emma, I get the
following output:

Died: emma uses external program 'clustalw' which is not in the PATH or
defined as EMBOSS_CLUSTALW

I can confirm that my jemboss.properties file
(\$EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties)
correctly points to the root directories of the clustalw and primer3
binaries e.g.:

embossPath=/path/to/clustal:/path/to/primer3

Can I also expect the same problem with the external primer3 binary?
Presumably the same solution for clustal will work for primer3?

Also, and I suspect I know the answer to this question, I'm attempting
to input a test file into emma with the following contents:

SWISSPROT:PA1_HUMAN
SWISSPROT:PAX1_HUMAN
SWISSPROT:PAX2_HUMAN
SWISSPROT:PAX3_HUMAN
SWISSPROT:PAX4_HUMAN
SWISSPROT:PAX5_HUMAN
SWISSPROT:PAX6_HUMAN
SWISSPROT:PAX7_HUMAN
SWISSPROT:PAX8_HUMAN
SWISSPROT:PAX9_HUMAN
SWISSPROT:PAXI1_HUMAN

I pre-pended the path to this file with an @ to indicate that it's a
list file e.g.:

@C:\path\to\multiple\sequence\alignment\file.sw

Am I correct in assuming that even when I've resolved the path issue to
the clustalw binary, I need a locally installed database (or URL to an
external database) for this analysis to run successfully? If so, how do
I prepare/install/configure my system to access this database (Swiss-Prot)?

Many thanks for your time and help.

Best regards,

Nigel Binns

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