Checking for bad dna sequences

[adriaan]

hi all,
I have an assignment were I have to check multiple human dna sequences that look like this

ORIGIN

1 ttgctgcaga cgctcacccc agacactcac tgcaccggag tgagcgcgac catcatgtcc
61 atgctcgtgg tctttctctt gctgtggggt gtcacctggg gcccagtgac agaagcagcc
121 atattttatg agacgcagcc cagcctgtgg gcagagtccg aatcactgct gaaacccttg
181 gccaatgtga cgctgacgtg ccaggcccac ctggagactc cagacttcca gctgttcaag
241 aatggggtgg cccaggagcc tgtgcacctt gactcacctg ccatcaagca ccagttcctg
301 ctgacgggtg acacccaggg ccgctaccgc tgccgctcgg gcttgtccac aggatggacc //

the dan starts at origin and ends at // ,
What I have to find are sequences that represent diseases like for example this one :
gcttgtccac atattttatg agacgcagcc

Now this isn't that hard but the problem is that the to be found sequences can be expanded over several lines and i have to be able to return in witch lines they were encountered and at witch position.

thanx in advance

adriaan

[eWish]

Welcome to TSDN!

Is this homework? If so,please read our Posting Guidlines. Please post your code that you have tried. Also, have a look at CPAN for a module to assist in what you are doing.

--Kevin

[adriaan]

thanks for the reply
youre link to
http://serach.cpan.org/
doesn't seem to work so I don't know what you mean with the module thing.
It's not really homework, it's more of an exercise I was advised to try out
on.
this the code i've written to get the evil sequences out of the database,
I don't really have any usefull code yet on the analyzing section as Im still trying to figure out how to do it

sub haalDataBaseOp
{
 
    open (DataBase,"database.txt");
 
    @data = <DataBase>;
 
    foreach $ziekte (@data)
    {
 
 
        # steek alle ziekte codes in een array
        if($ziekte =~ m/(\b[ctga]+\b)(.*)/)
        {
 
            $code = $1.$2; 
 
            #    print $code."\n";
 
        }
 
        # haal het nummer en de naam uit de string
        if($ziekte =~ m/(\d+)(.*?)(\b[gtac]+\b)/)
        {
 
            # nu maken we een hash met het nummer als keyword naar de ziekte naam
            $ziektenaam{$1} = $2;
 
            print $1."\n";
 
            print $code."\n";
 
            print $2."\n";
 
            # we maken ook een hash waarbij het nummer verwijst naar de gevonden ziekte codes
            $ziektecode{$1} = $code;
 
        }
 
    }
 
}

oh yes I'm a Belgian, so I nativly speak dutch and use that in my comments

[eWish]

Sorry, about the link to CPAN. I have corrected it. There are serveral bioinformatics modules available that would be designed to handle your request. Also, check out BioPerl.org, in the long run it will be a better solution.

--Kevin

[nithinpes]

As a reply to your initial posting where you wanted to search the pattern:
gcttgtccac atattttatg agacgcagcc (e.g) which can extend across multpile lines and to return the line number and position, the following code works:

$/ ="//";  ## input record separator: each sequence ends with //
open(DB,"database.txt") or die "sorry:$!";
$pos=0;
$line=1;
while(<DB>)
{
   ## \1 is to back refer pattern inside parantheses, which searches for 
   # newline  followed by digits 
   while(/\bgcttgtccac\b(\s*\n\d+)?\s+\batattttatg\b\1?\s+\bagacgcagcc\b/g)
{
    $prev=$`;                              # get the pattern preceeding your match
    $line++ while($prev=~/(\n)/g);  # increment whenever newline occurs
    @pos= split//,$prev;
    foreach (@pos)
        {$pos++ if(/[atgc]/);}         # get the number of residues preceeding match
    print "\n line:$line";
    print "\n position: $pos";
    $line=1;   $pos=0;                # reinitialize variables
}
 
}
 

Regards,
Nithin

[numberwhun]

As a reply to your initial posting where you wanted to search the pattern:
gcttgtccac atattttatg agacgcagcc (e.g) which can extend across multpile lines and to return the line number and position, the following code works:

$/ ="//";  ## input record separator: each sequence ends with //
open(DB,"database.txt") or die "sorry:$!";
$pos=0;
$line=1;
while(<DB>)
{
   ## \1 is to back refer pattern inside parantheses, which searches for 
   # newline  followed by digits 
   while(/\bgcttgtccac\b(\s*\n\d+)?\s+\batattttatg\b\1?\s+\bagacgcagcc\b/g)
{
    $prev=$`;                              # get the pattern preceeding your match
    $line++ while($prev=~/(\n)/g);  # increment whenever newline occurs
    @pos= split//,$prev;
    foreach (@pos)
        {$pos++ if(/[atgc]/);}         # get the number of residues preceeding match
    print "\n line:$line";
    print "\n position: $pos";
    $line=1;   $pos=0;                # reinitialize variables
}
 
}
 

Regards,
Nithin

First, when posting code into the forums, please be sure and use the proper code tags. That way, we moderators don't have to clean up behind you and add them to what you just posted. (As I have done here).

Next, just out of curiosity, have you checked out the bioperl website? I have seen this site referenced to others working with genomics and such and they ahve always said it was very helpful.

Regards,

Jeff

[nithinpes]

Hi Jeff,

I'm sorry for that. I have checked bioperl website, that's indeed very helpful in the long run.

Regards,
Nithin