[Bioperl-l] Simple Sequence alignment, StandAloneBlast build failure, and also seeking advice

[Demian Riccardi]

Hello,

Does BioPerl provide a method for calculated sequence identity or does that
only exist via external programs, such as Blast+?  I followed along with
the AlignIO_and_SimpleAlign HowTo, but Bio::Tools::Run::StandAloneBlast is
failing to build
...

------------- EXCEPTION -------------

MSG: Unknown version output: blastdbcmd: 2.7.1+

 Package: blast 2.7.1, build Oct 18 2017 20:40:57

....

which is a little frustrating. A nice slow method would be just fine for a
proof of principle for now, but I can't find one.

Below is a little script displaying my dream (it uses a DBIx::Class
database I wrote that has a bunch around 80K sequences that I'd like to
play with using BioPerl). Any advice is appreciated. My apologies if I
failed to find something obvious in the docs or how tos!

Thanks,
Demian

use Modern::Perl;

use lib 'lib';


use CysDB::Schema;

use Bio::Seq;

use Data::Dumper;


my $schema = CysDB::Schema->connect('dbi:SQLite:cys.db');


my $chain1 = $schema->resultset('ChainCys')->find({id => 1} );

my $chain3 = $schema->resultset('ChainCys')->find({id => 3} );


my $seq1 = Bio::Seq->new(-seq => $chain1->sequence, -alphabet => 'protein');

my $seq3 = Bio::Seq->new(-seq => $chain3->sequence, -alphabet => 'protein');

#my dream

say some_align_function_returning_alignobject($seq1,$seq3)->percent_identity


# Problem area comment

#use  Bio::Tools::Run::StandAloneBlast;


#$factory = Bio::Tools::Run::StandAloneBlast->new(-outfile => 'bl2seq.out');


#my $bl2seq_report = $factory->bl2seq($seq1, $seq2)


#print Dumper $bl2seq;
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