Module

[Rita]

i have 2 sequences like
ASDFGHJKLOIUYTREWQ and
ASDHJKLTREWQ

so when we align both sequence there is some GAP like
FG
OIUY.
so is there some module which can find this type of gap sequences.
thanks

 

[usenet]

i have 2 sequences like
ASDFGHJKLOIUYTREWQ and
ASDHJKLTREWQ

In your example data, the second sequence comprises a subset of the
first. Will this always be the case? Or could you have sequences like
this:

ASDFGHJKLOIUYTREWQ
ASabcDHJKLTREWQ

where the second sequence has elements not found in the first?

 

[Rita]

In your example data, the second sequence comprises a subset of the
first. Will this always be the case? Or could you have sequences like
this:

ASDFGHJKLOIUYTREWQ
ASabcDHJKLTREWQ

where the second sequence has elements not found in the first?

no. second one is always subsequence of first one

 

[Eden Cardim]

Rita escreveu:

i have 2 sequences like
ASDFGHJKLOIUYTREWQ and
ASDHJKLTREWQ

so when we align both sequence there is some GAP like
FG
OIUY.
so is there some module which can find this type of gap sequences.
thanks

I can tell from your posts that you're into bioinformatics. The tool
you're looking for is called BLAST (Basic Local Alignment and Search
Tool) and can be found at NCBI (http://www.ncbi.nlm.nih.gov/BLAST/).
The Bioperl project (www.bioperl.org) provides modules with several
bioinformatics tools, including a front-end for BLAST. You can get all
the latest bioperl modules from CPAN.

 

[Rita]

Rita escreveu:


I can tell from your posts that you're into bioinformatics. The tool
you're looking for is called BLAST (Basic Local Alignment and Search
Tool) and can be found at NCBI (http://www.ncbi.nlm.nih.gov/BLAST/).
The Bioperl project (www.bioperl.org) provides modules with several
bioinformatics tools, including a front-end for BLAST. You can get all
the latest bioperl modules from CPAN.

thanks,i know about BLAST but after BLAST i want the sequence whis is
not aligning so is there any module for that.

 

[Eden Cardim]

thanks,i know about BLAST but after BLAST i want the sequence whis is

not aligning so is there any module for that.

Oh, now I understand what you want, the solution is simple so I don't
think anyone would have coded a specific module for that, maybe you can
find a toolkit at CPAN. Here's a way to get at the gaps in the
sequences:

($gap) = $sequence =~ /$match1(.+?)$match2/;

 

[Rita]

Oh, now I understand what you want, the solution is simple so I don't
think anyone would have coded a specific module for that, maybe you

Thank you so much for your help! I couldn't figure it out.

 

[Rita]

Oh, now I understand what you want, the solution is simple so I don't
think anyone would have coded a specific module for that,

It looks like you Know about Bioinformatics.i started to do it and i
red the book that Beginning Perl for Bioinformatics.but i think ,i
should read some more books or online documents about it so can you
sggest me some name .

($gap) = $sequence =~ /$match1(.+?)$match2/;

what will be value of $sequence and $match1 ,$match2.
and if i have more than 1 gap in my sequence then is it find that too
or i have to put in a loop or something.
thanks

 

[Eden Cardim]

It looks like you Know about Bioinformatics.i started to do it and i

red the book that Beginning Perl for Bioinformatics.but i think ,i
should read some more books or online documents about it so can you
sggest me some name .

amazon.com
search for books with "perl bioinformatics"

what will be value of $sequence and $match1 ,$match2.

an example with the data you provided previously:

$sequence = "ASDFGHJKLOIUYTREWQ";
$match1 = "ASD";
$match2 = "HJKL";
($gap) = $sequence =~ /$match1(.+?)$match2/;
#$gap now contains "FG";

and if i have more than 1 gap in my sequence then is it find that too
or i have to put in a loop or something.
thanks

yes, you need a loop, I haven't dealt directly with BLAST output for a
long time now so I'm not sure how it represents alignment gaps, I think
it uses '-', so you would need to split on that.
I suggest you do some more reading about Perl before actually building
production code.

 

[Rita]

amazon.com
search for books with "perl bioinformatics"


an example with the data you provided previously:

$sequence = "ASDFGHJKLOIUYTREWQ";
$match1 = "ASD";
$match2 = "HJKL";
($gap) = $sequence =~ /$match1(.+?)$match2/;
#$gap now contains "FG";


yes, you need a loop, I haven't dealt directly with BLAST output for a
long time now so I'm not sure how it represents alignment gaps, I think
it uses '-', so you would need to split on that.
I suggest you do some more reading about Perl before actually building
production code.

thanks