OMA Blog

New Release with 1109 genomes is here

2011-05-18T09:33:00.004+02:00

The May 2011 release of OMA consists of 1109 genomes is now online. The interruption of the OMA Browser was only for a short time, now everything should work well.

The current release contains many new and updated plant (Cassava, Rice, Ostreococcus) and insect genomes (Louse, Mosquito, Aphid, several Flies), the Giant Panda and various new Archaea and Bacterias.

From this release on, we also provide cross-references to Refseq and EntrezGene identifiers for protein sequences which are identical.

Coming up: new release with 1109 genomes

2011-05-16T08:54:00.002+02:00

Good news! We have finally finished the computation of a new data set with 1109 genomes.

The new data set will be available in the OMA Browser within the next two days. This can cause short interruption of the web server. Sorry for any inconveniences. The data of the current release will be available in the OMA Browser Archive.

New Release (Nov 2010)

2010-11-11T11:06:00.007+01:00

We're pleased to announce the 11th release (Nov 2010) of OMA.

For this release, we added a new grouping strategy: Apart from the OMA groups, we now also provide hierarchical groups containing orthologs and inparalogs within a user selectable taxonomic range.

We have also added a new consistency criterion for our pairwise ortholog predictions, which assures that the predictions between a pair of genomes are biological consistent. Due to this new criterion, we corrected a small fraction of our predictions.

New release (May 2010) is here

2010-06-02T08:32:00.003+02:00

The May 2010 release of OMA with 1000 genomes is now online. The interruption of the OMA Browser was only for a short time, now everything should work well.
The data of the previous releases is still available for download.

Coming up: new release with 1000 genomes

2010-05-26T09:18:00.002+02:00

We have finished the computation of a new data set, breaking the 1000 genomes boundary. Besides 93 new genomes (including metazoans such as the turkey, the pig or the marmoset), we again have updated more than 80 older genomes.

If all goes well, the new data set will be available in the OMA Browser sometime next week. This can cause short interruptions of the web server. If you are working on a project with the current data set, we recommend, that you download all the data you need before the change. However, the current release will still be available in the OMA Browser Archive.

IDs and Sequences of TETNG (Tetraodon nigroviridis) fixed

2009-12-07T14:11:00.005+01:00

Dear users,

we could fix the problems with the Tetraodon nigroviridis IDs and protein sequences. The OMA Browser is now up again and fully working.

We would like to express our sincere apologies for any inconvenience caused.

The OMA team

Warning: TETNG (Tetraodon nigroviridis) has wrong IDs/sequences in current release

2009-12-03T11:39:00.003+01:00

Dear OMA users,

Dr. Ingo Ebersberger (Center for Integrative Bioinformatics Vienna) brought to our attention that all TETNG (Tetraodon nigroviridis) IDs and sequences of the current release (October 2009) are wrong.

We are sorry for the trouble this may have caused.

At least, we found the bug, and we are confident that 1) no other species has the same problem, and 2) orthology predictions were not disrupted because of this problem.

We are now fixing the problem, and hope to have a new release ready by early next week. In the meanwhile, the other species should be fine.

Thanks to Ingo for reporting the problem, and to all of your for your understanding.

The OMA team

OMA Survey: we have a winner

2009-11-30T14:29:00.005+01:00

First, we would like to thank all of you who participated in the survey. We received lots of constructive feedback. We will try to improve the OMA browser accordingly.

As promised, we drew a random entry from the responses, and the lucky person turned our to be... Dr. Albert Vilella from the Ensembl Compara team at EBI. Needless to say, we are delighted to see the iPod go to one of our best competitors... :-)

Thanks again to all of you. And don't wait for the next survey to send us any additional feedback you might have!

New release is here

2009-10-30T16:14:00.003+01:00

The October 2009 release of OMA with 907 genomes is now online. The interruption of the OMA Browser was only for a short time, now everything should work well.

There is a slight change in the way alternative splicings are treated. From the current release on, only one splicing variants of a gene can have orthologs (we chose the one with the most matches in other genomes). This should have the effect that groups are more complete> Before, the different splicings variants had the tendency to be scattered among several groups.

And finally, we would like to point out again the survey on the OMA Browser. We really like to know your opinion so we can improve the OMA Browser. And you have the chance to win an iPod. Go here to fill out the survey, it won't take more than 5-10 minutes.

Coming up: new release with 907 genomes

2009-10-22T09:23:00.002+02:00

Good news! We have finished the computation of a new data set with 907 genomes. Besides 78 new genomes (including metazoans such as the sloth, the liziard, zebra finch or the tick), we also have updated 55 older genomes.

If all goes well, the new data set will be available in the OMA Browser sometime next week. This can cause short interuption of the web server. If you are working on a project with the current data set, we recommend, that you download all the data you need before the change. However, the current release will still be available in the OMA Browser Archive.

Fill out our survey and win a new iPod nano!

2009-09-30T13:43:00.007+02:00

Please help us improve your experience on the OMA Browser by taking our survey!

It has 15 questions and will only take you 5-10 minutes to fill out.

And as always, feel free to send us your feedback and suggestions by e-mail or in the comment section of this blog.

Coding DNA available for download

2009-08-17T15:52:00.003+02:00

We are pleased that we can start this blog with some good news: the coding DNA for all OMA proteins are now available for download in fasta files. We have split them into two files, one for eukaryotes and one for prokaryotes. They are available on the download page: http://omabrowser.org/All/download.html

First Post

2009-07-09T15:04:00.000+02:00

The famous first post! We will use this blog to publish news about OMA and the OMA Browser. Enjoy!