sequence retrieval

[yogeshwar]

hello all , i have data around 500000 seq of a plant and i wanna fetch some 37000 seq from my database ,but what i have is the name of query seq is there any perl program to perform this task ,as i am very new in field of computational genomics and biology.plz help me

[Rhizosis]

Could you exactly tell us what kind of data you have in your database?
What columns are populated?

If you have the names of the 37000 sequences you would like to extract, you can query the database (assuming its a generic SQL database) quite easily.

Please provide a bit more info.

[Rhizosis]

If you have your names of the query sequences in a newline delimited txt file something like the following might help:

#!/usr/bin/perl -w
use DBI;
use strict;
use warnings;

my $dbh = DBI->connect('dbi:mysql:perltest','root','password')
 or die "Connection Error: $DBI::errstr\n";

my $sql;

while(<>){
 my $seq_name = chomp($_);
 $sql = "select seqColName from tableName where queryName='$seq_name'";
 $sth = $dbh->prepare($sql);
 $sth->execute
 or die "SQL Error: $DBI::errstr\n";
 
 print "Query Name: \t Sequence:";
 while (my @row = $sth->fetchrow_array) {
     print "$seq_name\t$row[0]\n";
 } 
}

Hope it helps. Otherwise you should provide more info.

[yogeshwar]

well, i have large amount of fasta seq in my database, and i want to retrieve around 37000 seq of my interest from it , as i am a fresher in bioinformatics and genomics , i have very little idea to do this task using perl coding , that why i really want a perl code who can perform this task.
And that's why i need ur help

[Rhizosis]

Well I can give you the answer without a problem. But its important to learn from it yourself too! Especially in the world of bioinformatics.

Could you layout what your database structure is like? On the command line login to your Mysql database and then type:
DESCRIBE name_of_table_with_fasta_seqs;

Whats the structure like, what database are you running? What OS are you running?

All kind of relevant here.

[GenoMax]

well, i have large amount of fasta seq in my database, and i want to retrieve around 37000 seq of my interest from it

Are your sequences in a real "database" or are you referring to a file/web accessible resource?