Changes to mysqlimport

Owing to problems with BLOB data in some tables, we have had to change the way these tables are dumped, which in turn means a change to the mysqlimport parameters.

It has been necessary to escape the table fields when dumping the MySQL text files. Hence to import successfully, a field escape parameter needs to be specified when using mysqlimport, e.g.

mysqlimport -h your_host -u write_user -p write_pass -P 3306 --fields_escaped_by=\\ database_name /full/path/to/table_name.txt

Tables affected in Release 59 are:

* homo_sapiens_funcgen_59_37d.result_feature
* mus_musculus_funcgen_59_37l.result_feature
* ensembl_compara_59.conservation_scores

and the meta_conf__xml__dm and meta_template__xml__dm tables in all mart databases.

From release 60, all Ensembl mysql dumps will be done this way, so you will need to use the above parameters on all imports.

Ensembl Events in October 2010

In October we have the following Ensembl events:

12 Oct: Ensembl module in the EBI Bioinformatics Roadshow, Dokuz Eylul University, Izmir, Turkey
13 Oct: Tutorial for The National Genetics Reference Lab, Manchester, UK
14 Oct: Ensembl module in the EBI Bioinformatics Roadshow, Dokuz Eylul University, Izmir, Turkey
19 Oct: Tutorial for The National Genetics Reference Lab, Manchester, UK
19 Oct: Browser workshop at the Royal Veterinary College, Potters Bar, UK *postponed to 26 Oct*
22 Oct: Browser workshop at the Free University Brussels, Belgium

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Changing to LASTZ

People following the declarations of intentions for the next release (these are sent to announce@ensembl.org) may have noticed that we are releasing LASTZ pairwise alignments instead of BLASTZ ones. LASTZ is written by Bob Harris from the Penn State University as a replacement of BLASTZ, as BLASTZ is now considered obsolete (read the announcement).

This is the first release where we use LASTZ for the new alignments. We will update the previous alignments in the following releases.

A.mel vs A.mel

Ensembl is already working on the forthcoming release (e60!). The declaration of intentions have been published and include the new Giant Panda (Ailuropoda melanoleuca) genome.

While I was looking at the alignments we are planing to release, I saw the H.sap-A.mel LASTZ-net alignments. Hey! I thought we banned Apis mellifera from Ensembl long time ago.

Then I realised that the scientific names of both the honey bee and the giant panda start with the same letters. So, don't get confused, one of them eats flowers and makes honey, while the other one eats bamboo and makes very nice teddies!

Tell Us What You Think!

To new and frequent Ensembl users,

We are continuously striving to improve our web interface at www.ensembl.org.

Please let us know how we're doing!

The survey should take 10-15 minutes.

http://www.surveymonkey.com/s/KCR6WN2

Many thanks,
The Ensembl Team