Category: "mySQL"

Public Ensembl databases

July 5th, 2011
A quick reminder of the specifications to connect to the public Ensembl mySQL databases: Database Server Port Ensembl Genomes, all databases mysql.ebi.ac.uk 4157 Ensembl (v 24-47) ensembldb.ensembl.org 5306 Ensembl Mart martd… 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 »

Ensembl Core Database Schema Diagram

November 26th, 2010
To understand the concept of Ensembl and learn how to query the tables I find it extremely useful to have a schema diagram of the database in front of me. This can be generated by using the schema.sql and foreign_keys.sql files from the sql directory… more »

mySQL Data Types

March 6th, 2009
Ty p e S i z e D e s c r i p t i o n CHAR[Length] Length bytes A fixed-length field from 0 to 255 characte… more »

Ruby & MySQL

January 12th, 2009
Using MySQL from Ruby Ruby can connect to a MySQL database using the Ruby/MySQL module. There is a complete introduction into the subject can be found here: http://www.kitebird.com/articles/ruby-mysql.html The core functions of the modules are explained… more »