Question: Convert Blastall cmd to Blast+
1
gravatar for cowmoomoo
4.1 years ago by
cowmoomoo10
United States
cowmoomoo10 wrote:

Hi, 

I'm trying to convert an old blastall script (the older version of Blast that NCBI recommends people to upgrade from) to a blast+ command, 

I've tried using the NCBI's legacy_blast.pl command to generate the new blastall script, but I'm still getting different results,  

#legacy blastall
./legacy_blast.pl blastall -i query.fasta -d /path/to/blastdb -o blastResult.blast -m 7 -e 1.00000e-10 -b 5 -v 5 -p blastx -Q 11 -S 1 -F "M s" --print_only
#converted blast+ cmd
/usr/bin/blastx -db /path/to/blastdb -query query.fasta -evalue 1.00000e-10 -num_descriptions 5 -num_alignments 5 -query_gencode 11 -out blastResult.blast-outfmt 5 -seg yes -soft_masking true

It would seem like all the parameters line up, however when I look in the Blast output file, I see the results to be slightly different and also the filter parameters might be different, the blastall has only "F" as parameter filter while blast+ has "L;m" for parameter filters,

#legacy blastall blast result xml output

    <Parameters>

      <Parameters_matrix>BLOSUM62</Parameters_matrix>

      <Parameters_expect>1e-10</Parameters_expect>

      <Parameters_gap-open>11</Parameters_gap-open>

      <Parameters_gap-extend>1</Parameters_gap-extend>

      <Parameters_filter>F</Parameters_filter>

    </Parameters>

  </BlastOutput_param>

<BlastOutput_iterations>

<Iteration>

vs:

#legacy blast+ result xml output

    <Parameters>

      <Parameters_matrix>BLOSUM62</Parameters_matrix>

      <Parameters_expect>1e-10</Parameters_expect>

      <Parameters_gap-open>11</Parameters_gap-open>

      <Parameters_gap-extend>1</Parameters_gap-extend>

      <Parameters_filter>L;m;</Parameters_filter>

    </Parameters>

  </BlastOutput_param>

<BlastOutput_iterations>

<Iteration>

Anyone have an idea what I"m missing and what other flags I need to add to the blast+ command to get it to get the same results as the original blastall cmd?

Thanks in advance for your time and help!

blast alignment genome • 2.1k views
ADD COMMENTlink modified 4.0 years ago by h.mon27k • written 4.1 years ago by cowmoomoo10
0
gravatar for 5heikki
4.0 years ago by
5heikki8.5k
Finland
5heikki8.5k wrote:
       This script converts and runs the equivalent NCBI C toolkit command

       line BLAST program and arguments provided to it (whenever possible) to

       NCBI C++ tookit BLAST programs. Note that to specify options to this

       script they MUST use 2 dashes to prefix the options AND be listed at

       the end of the command line invocation to convert.
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by 5heikki8.5k
0
gravatar for h.mon
4.0 years ago by
h.mon27k
Brazil
h.mon27k wrote:

Although I am not sure, I guess it is not possible to guarantee identical outputs from BLAST+ and legacy BLAST - many things changed along the way, not all of them in a backward-compatible manner. I remember reading about issues similar to yours on the blog Blasted Bioinformatics.

ADD COMMENTlink written 4.0 years ago by h.mon27k
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