[Inparanoid] BLASTALL and inparanoid

Chibucos, Marcus MChibucos at som.umaryland.edu
Fri May 25 01:49:59 CEST 2012

Hello Tom,

I am not affiliated with InParanoid, and I am only an end user like yourself. However, I have a suggestion that might prove helpful, if you are willing to tinker a bit. (It worked for me, but I'd be curious if the InParanoid developers advise against this for some reason...)

I ran BLAST independently of InParanoid, as I had many proteomes to compare and I wanted to distribute the BLAST jobs on my institute's grid. I then used the BLAST outputs as inputs into InParanoid's blast_parser.pl script, and finally ran InParanoid. To achieve this, I did the following:

1. Run BLAST by whatever means you like, specifying to generate outputs in XML format. (I used that blastall program, but I don't see why this won't work with blast+ provided you specify XML output. For blastall, I specified these parameters, in addition to the query and database: -e 1e-1 -F 'm S' -b 20 -v 20 -M BLOSUM62 -m 7)

2. Feed the resulting BLAST XML files into the blast_parser.pl script that comes with InParanoid, as follows. Notes: (a) my FASTA files and BLAST outputs are named without extensions; for example, species a is called "a" (not "a.fa") and species a vs. species b is simply called "ab" (not "ab.xml"). (b) All BLAST outputs are in a sub-directory called "blast_results". (c) To be safe, I backed up my BLAST results before I tried this, since it takes a long time to run the BLAST searches...

In a BASH terminal (command line), from the main directory, do this:

cat blast_results/ab | ./blast_parser.pl 0 > ab

This will read the BLAST output called "ab" from the sub directory "blast_results" and pass it to the blast_parser.pl script in the main directory, which will generate an output file called "ab" in the main directory. I parsed multiple XML files with a simple BASH script run from the main directory to automate the process, like this:

 for i in aa ab bb ba ac bc # [et cetera - add any number of files here]
 cat blast_results/$i | ./blast_parser.pl 0 > $i

3. Set the variable to turn off BLAST inside the InParanoid file (line 44 or 45): $run_blast = 0

4. Run InParanoid (using outgroup in my case): ./inparanoid.pl a b c

I hope that is helpful.

Best regards,
Marcus Chibucos

On 5/24/12 10:15 AM, de Man, Tom wrote:
Dear people from inparanoid,

The first step of inparanoid is performing a BLASTALL run, however the new BLAST+ does not contain BLASTALL anymore.
With this reimplementation of BLAST you deal with separate programs.

At the original BLAST you use commands like: BLASTALL -p blastp. However with BLAST+ you can run blastp as a program instead of using it as a parameter of BLASTALL. Is there a version of inparanoid that can handle this new BLAST or should I just use an older version of BLAST with BLASTALL included.

Many thanks for your reply.

Kind regards,
Tom de Man


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