Category: "Perl"

Parsing OMIM data

April 18th, 2011
------------- EXCEPTION ------------- MSG: 16.13.3 does not make sense: 'arm' or 'cen' missing STACK Bio::Map::CytoPosition::cytorange BioPerl-1.6.0/Bio/Map/CytoPosition.pm:165 more »

PAR regions

April 6th, 2011
To pull out the coordinates of the pseudo-autosomal regions from the Ensembl database, you can perform the following query on the core database: select sr.name as chromosome, ae.seq_region_start as start, ae.seq_region_end as end from assembly_exceptio… more »

PDL: The Perl Data Language

March 1st, 2011
The Perl Data Language is a Perl extension for numerical manipulation that provides the convenience of Perl with the speed of compiled C. quick start pages. perl docs more »

Submitting to EMBLdb

January 24th, 2011
To submit DNA sequences from capillary (Sanger) sequencing to the public EMBL database, these steps can be take: Webin submission page: http://www.ebi.ac.uk/embl/Submission/webin.html -> create 1 submission (Hx2000011028), send the rest in batch… more »

Caching in ENSEMBL

November 11th, 2009
How to avoid falling in the cache... Caching is a powerful way to speed up queries to the Ensembl database. It can get problematic however for example if you are repeating a query multiple time, but have updated the data set in between. It is importa… more »