Go Back   Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum > Molecular Research Topics Forum > Bioinformatics
Register Search Today's Posts Mark Forums Read

Bioinformatics Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.

cnv map to gene

cnv map to gene - Bioinformatics

cnv map to gene - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.

LinkBack Thread Tools Display Modes
Old 04-23-2012, 07:04 PM
Pipette Filler
Points: 99, Level: 1 Points: 99, Level: 1 Points: 99, Level: 1
Activity: 0% Activity: 0% Activity: 0%
Join Date: Mar 2012
Posts: 2
Thanks: 0
Thanked 0 Times in 0 Posts
Default cnv map to gene


I am trying to find overlap between CNV genomic region(start and stop bp position) and genes(start and stop bp position). Overlap can be in different ways: i). either there wont be any overlap i.e the gene region will not fall in the CNV region or ii). it will fall completely within the region or iii) it may fall partially i.e gene region might overlap with the CNV start position or gene region overlapping with the stop postion of the CNV. So if there will be an overlap it will return 1 and if not then it will return 0 and the output file finally will have all the overlap and the gene name with which this cnv region is overlapping.
So I am reading in the main CNV file and two other gene list files.

Am I doing this correctly? Any suggestions?


#Open the cnv file with start, stop

my $input_gene_file = "path to file";
die "Cannot open $input_gene_file\n" unless (open(IN, $input_gene_file));

my %size_CNV_start_CNV_stop;
while (chomp($line = <IN>))
my (@columns) = split /\s+/, $line;
my $size = $columns[3];
my $CNV_start = $columns[1];
my $CNV_stop = $columns[2];
$size_and_CNV_start{$size} = $CNV_start;
$size_and_CNV_stop{$size} = $CNV_stop;

#Now open files for genelist1 and genelist2 with respective start and stops

open (MYFILE, "path to file");
@file1 = <MYFILE>;
close MYFILE;
open (MYFILE2, "path to file");
@file2 = <MYFILE2>;
close MYFILE2;

foreach $line (@file1,@file2){
sub overlap {
my ($CNV_start, $CNV_stop, $Gene_start, $Gene_stop) = @_;
if ($Gene_stop < $CNV_start || $Gene_start < $CNV_stop) {
return 0;
if (Gene_stop > $CNV_start || $Gene_stop > $CNV_stop){
return 1;

#Open output file and write the locations of each symbol
die "output.txt" unless(open( OUT,"> output.txt"));

while (defined($symbol = <IN>))

my $CNV_start = $size_and_CNV_start{$size};
my $CNV_stop = $size_and_CNV_stop{$size};
print OUT " $size\ $CNV_start\ $CNV_stop \n";
Reply With Quote

cnv , gene , map

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On

Forum Jump

Similar Threads
Thread Thread Starter Forum Replies Last Post
Human Cytome Project - Update 24 Jan. 2005 Peter Van Osta Cell Biology and Cell Culture 1 08-01-2010 02:18 PM
New Saccharomyces Sequences 11/27/04 Mike Cherry Yeast Forum 0 11-29-2004 12:39 AM
New Saccharomyces Sequences 09/08/04 SGD Sequences Yeast Forum 0 09-13-2004 10:07 PM
New Saccharomyces Sequences 08/11/04 SGD Sequences Yeast Forum 0 08-12-2004 12:26 AM
New Saccharomyces Sequences 05/19/04 SGD Sequences Yeast Forum 0 05-23-2004 04:06 PM

All times are GMT. The time now is 06:44 AM.

Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2015, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved
Page generated in 0.16100 seconds with 16 queries