BioPerl/Linux basic and programming

Question

[Mohamed]

Dear All,

I've just installed Bioperl. I am completely new to such kinds of software. I have few questions:

1. How to inform Bioperl that my fasta file is in a specific location and to use it for restriction digestions or to use it for Blast or other functions. (I am using Bioperl for windows 7).
2. How to make a script file in Linuix. I mean in windows, I can open notepad and save the file as (ex.pl). Now, in Linux, how to save the file with such extension. Or it is not necessary and Linux identify it.
3. Last and very important to me, can anyone kindly inform me how to extract specific sequences from a fasta file saved on my hard disk and from a certain start position to a specific end position and save it as text or Excel file using Bioperl. I have a list (file in Excel) of predicted genes from a bacterial genome.

Thank you.

Mohamed

[Mohamed]

Dear Michael,

Thanks a lot for your kind and quick response. Many thanks too for the quick and clear advise regarding Linux.

Just I wish to add that I already went to the mentioned website but (it might be my own problem), it does not give clear working example. I am just starting Linux/Unix programs and thus it took me ages to understand how things go. For Biochemists/Biologists, might be better, to kindly demonstrate things in a clear simple way (with videos, if possible).

It just give a sample script. It is better if they kindly provide a complete working exmple (like for example what happen if you watched any Lynda videos).

Best regards,
Mohamed

[Michael]

I can give you a little example, but it would be easier if you could also define more specifically what the actual problem is. This is best done by showing what you have already tried with an example script. There are for sure video tutorials on BioPerl if you like this approach, they might have advantages, a clear disadvantage is that you cannot just copy-paste code directly from the video.

[Mohamed]

Dear Michael,

Again, that is too kind from you. I know that I should do my homework first before starting complaining. And that I am also responsible for my own problem. I just was expecting more simple and educational way for teaching Bioperl to beginners (or even less than this).

The project I am working on: is that to search one bacterial genome for predicted genes, then to isolate that predicted genes and locations with their sequences and their positions. So, it seems that I need to know how to download, save, fetch back that file, and run the scripts to extract the sequences.

Thanks for your support and I am very sorry for the long response.

Mohamed

Answer 1

[Michael]

I suggest to go through a number of tutorials first to answer your question yourself:

1. e.g.: http://www.bioperl.org/wiki/HOWTO:Beginners and http://www.bioperl.org/wiki/HOWTO:SeqIO
2. any basic Linux tutorial (this question part is off-topic for this site, short answer: suffix has no relevance (only for you))
3. use method subseq on Bio::Seq objects: http://search.cpan.org/~cjfields/BioPerl-1.6.923/Bio/Seq.pm#subseq

Here is a little example script (all information is also found in the documentation), what to do further on depends on a more exact description of the problem:

/usr/bin/env perl
use strict;
use warnings;

use Bio::SeqIO;

# This is the main sequence object in Bioperl
# gets a sequence from a file
my $seqio  = Bio::SeqIO->new( '-format' => 'fasta' , -file => '/home/joeuser/myfile.fasta');

while (my $seqobj = $seqio->next_seq()) {

   # gets sequence as a string from sequence object
   my $seqstr   = $seqobj->subseq(10,50); # slice in biological coordinates

         ### do something with seqstring

}