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Old 01-23-2014, 05:17 PM   #1
bio_informatics
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Location: USA

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Posts: 182
Default help with topcons membrane prediction

Hi,

I have been trying to use topcons membrane prediction.
I am trying to run the consensus one, but I am stuck with

Code:
run_blast.sh
of octopus.
I am stuck at this.
Running topcons is a 3 step process:
1) get file from run_blast.sh
2) process that output for modhmm profile
3) create .mtx file

The read_me file doesn't say clearly.
It has instructions based on OLDER version of Blast.

Can someone please help me with this?

There is an other way round this:
1) run_topcons_single.sh
2) run_topcons.sh

I fail to understand which one to use and how.

I have the dependencies for TOPCONS.sh in my PATH.

I need this prediction on standalone tools.
I have a protein file with 35 protein sequences and I have 20 such files.

Any help shall be greatly appreciated.
Thank you.
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Old 01-24-2014, 03:29 AM   #2
TiborNagy
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Posts: 329
Default

You get an error message? Please add more details about you problem.
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Old 01-27-2014, 04:58 PM   #3
bio_informatics
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Location: USA

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Posts: 182
Default

I get error as:

Directory /home/robber/bin/../var/www/topcons.cbr.su.se/docroot/topcons/ does not exist

However, the aboce directory exists in the location.
I have added that location in my PATH as well.

Quote:
Originally Posted by TiborNagy View Post
You get an error message? Please add more details about you problem.

Last edited by bio_informatics; 01-27-2014 at 05:48 PM. Reason: Error more clear
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