I've seen this question asked and partially answered all around the web. As with anything related to Perl, I'm sure there is more than one way to do it. Here's how I do it with Perl 5.10.1 on CentOS 6.4. First, install local::lib with bootstrapping method as described here.

NCBI has put a lot of effort into unifying their data access and retrieval system -- whether you are searching for a gene, protein, or publication, the results are returned in a similar fashion.

Obtaining the probability that zero, one, or two alleles are shared identical by descent (IBD) is useful for many reasons in a GWAS analysis. A while back I showed you how to visualize sample relatedness using R and ggplot2, which requires IBD estimates. Using plink --genome uses IBS and allele frequencies to infer IBD.

Last week Will showed you a bash script version of a sed command covered here a while back that would convert PLINK output from the default variable space-delimited format to a more database-loading-friendly tab or comma delimited file. A commenter asked how to do this on windows, so I'll share the way I do this using a perl script which you can use on windows after installing ActivePerl.

This looks like a must-read for anyone starting out in computational biology without extensive experience at the command line.  The 135-page document linked at the bottom of the Google Group page looks like an excellent primer with lots of examples that could probably be completed in a day or two, and provides a great start for working in a Linux/Unix environment and programming with Perl.

In the last post I showed you how to point to a file in windows and get the full path copied to your clipboard.  I wanted to come up with something similar for a Linux environment.  This is helpful on Vampire/ACCRE because you have to fully qualify the path to every file you use when you submit jobs with PBS scripts.

And it will do way more than display "Hello, world!" to the screen. An anonymous commenter on one of our Linux posts recently asked how to write scripts that will automate the same analysis on multiple files. While there are potentially several ways to do this, perl will almost always get the job done.