[Bioperl-l] no blast result

Fields, Christopher J cjfields at illinois.edu
Tue Sep 13 15:36:21 EDT 2011

On Sep 12, 2011, at 9:00 AM, Peter Cock wrote:

> On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
>> looks like BLAST is not install on your system. The BioPerl module only
>> runs BLAST for you and parses the output but you still need the BLAST
>> executables installed on your system. Follow the instructions on the
>> NCBI website to download and install BLAST and try running it on the
>> commandline with the "blastall" command. If that works then you can run
>> it also via BioPerl.
>> Frank
> Hang on - blastall is from the "legacy" BLAST suite, does
> BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
> blastn and blastp rather then blastall)?
> Peter

(aside: thought I sent this the other day.  never mix grant writing and open source)

Both BLAST and BLAST+ are supported via different modules.  Some users don't want to use BLAST+ for various reasons, though this may soon be out of their control when NCBI eventually stops supporting legacy BLAST entirely.


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