Connect to Standalone Clustalw using perl (in program)

Question

[rajkishore.ouatbi]

Please inform me , how can I connect perl program to local clustalw for finding the Multiple Seq. Alignment of the entered fasta format seq. in the perl.

Answer 1

[Devon Ryan]

Just make your life easier and use bioperl, which has an interface to clustalw.

[rajkishore.ouatbi]

Fine .. I have installed bioperl (referring from web) but there's some error while running the libraries.

Will u say me the installation procedure in bioperl

[Devon Ryan]

The installation instructions for bioperl are provided here. If you run into an error, it would be helpful if you posted the actual error.

[rajkishore.ouatbi]

Yes installation was fine. But it was saved in tmp/bioperl.

But I was not getting the folder back in my system.

Rather when I runned a bioperl program it gives such an error.

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at msa.pl line 3.

Errors like -

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: id does not exist
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.14.2/Bio/Root/Root.pm:359
STACK: Bio::DB::WebDBSeqI::get_Seq_by_id /usr/local/share/perl/5.14.2/Bio/DB/WebDBSeqI.pm:154
STACK: Bio::Perl::get_sequence /usr/local/share/perl/5.14.2/Bio/Perl.pm:510
STACK: test1.pl:5
-----------------------------------------------------------

Please help .. !!

Unable to run bioperl ..!!

[rajkishore.ouatbi]

Is is not possible to call local clustalw in perl program ?? If yes please say me the procedure .. !! .

Thanks ..

[Devon Ryan]

There are likely a couple different ways to do that if you really needed. You could use named pipes and fork off a process to write to the second pipe (if you don't fork off a process, then you might situation where your program is blocked). Alternatively, just make and delete a pair of temp files for each call. Yet another alternative would be to see which shell "sh" is on your system and see if it has process substitution. Honestly, though, it'd be easier to just use bioperl.

[rajkishore.ouatbi]

Thanks Devon Ryan .. !!

Yes earlier also I was going through the same for the use of bioperl and also it seems to be quicker as compared to this process but I was confused in the installation procedure of bioperl because after installing it also there were some packages missing which creates error.

Mostly error like

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at msachk2.pl line 6.
BEGIN failed--compilation aborted at msachk2.pl line 6.

So , Unable to solve this all .. !! quiet interesting problems but .. time is a factor .. !! beyond to work.

Advice me please .. !!

[Devon Ryan]

A quick google search suggests that you just need to install the BioPerl-Run package in addition to BioPerl. Usually you can find the solution to things like this with a quick google search of the error message.