Category: "Bioinformatics"

Using dbVar

May 12th, 2011
dbVar is the NCBI database of genomic structural variation designed to store data on variant DNA ≥ 1 bp in size. Ids are organised in the following manner: (n|e)std: the study id - this identifies a submitted study (n|e)sv: the stru… 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 »

Sequence Contaminations

January 20th, 2011
A contaminated sequence is one that does not faithfully represent the genetic information from the biological source organism/organelle because it contains one or more sequence segments of foreign origin. [NCBI The primary approach to screening nucle… more »