Details of the changes since version 0.16 are posted to COTRASIF Google group.
Any further news are posted to that group as well. This page is only kept as an archive.
We have just updated all the genomes to Ensembl release 50. The delay with an update was due to some changes in the Ensembl field naming conventions.
Also, COTRASIF was presented at the 9th ICSB in Gothenburg, Sweden.
Within several days we plan to merge the two current servers (interface and workhorse) into a single one, and put it into a more reliable location. There will be one more notice on the exact expected downtime boundaries.
We are preparing the next COTRASIF version to be released soon after the move to the new server will be complete. Expected release date - not later than Septmeber, 30.
Severe electricity outage in the location of our working server lead to 11-hour downtime. Now everything is back to normal.
cotrasif Google group was created to facilitate feedback from COTRASIF users. This is a general group, where any feedback is welcome, including (but not limited to): criticism, technical questions, error reports, improvement suggestions, usability problems, usage questions, etc. To subscribe, send a letter to firstname.lastname@example.org; to unsibscribe, send a letter to email@example.com.
Group has open access policy, so that you only need to join (subscribe) if you want to write to the group; to read, you can just navigate to the group's page.
Conservation filter is now functional.
COTRASIF is now at version 0.14.
We integrated JASPAR database, and now you can insert TFBS matrix from the JASPAR drop-down menu. As with other COTRASIF components, JASPAR matrices will be regularly auto-updated to stay current.
JASPAR integration pushes COTRASIF version to 0.13.
All genomes updated to the latest Ensembl 49 release.
Tetraodon nigroviridis genome added.
We changed criteria for retrieving promoters from Ensembl, and now re-import promoters. New requirements do not set the filter "with EntrezGene ID only". This will allow importing more promoters from Ensembl.
For a short period, not all species will be available.
This news is an aggregate since last news.
COTRASIF is now version 0.12. It can now accept floating-point PSSMs/PFMs. Matrix verifier module is now more flexible and strict at the same time, and upon successful task submission the user is shown the exact matrix which will be used for search - to avoid "silent assumptions" hampering the repeatability of the search.
We also added new genome - Anopheles gambiae.
Help page was substantially extended over the past weeks, and now does offer some explanations on how COTRASIF works.
Input boxes are now pre-populated with examples; clicking in the input box selects all its content, to allow immediate pasting of own matrix/sequences.
Tasks submission process was improved: now, if there's and error in user's input, error message is shown together with pre-filled submission form.
Overall, we hope to have improved user experiences with COTRASIF a lot.
We are still working on the conservation tool, to finally make it a working part of COTRASIF.
All genomes updated to the recent Ensembl 48 release.
New genomes added: Saccharomyces cerevisiae (budding yeast) and Bos taurus (cattle), both Ensembl release 47.
As promised in the previous news yesterday, we have just fixed the overlapping promoters problem. Cleanup procedure is integrated into genomes import, so all new genomes will have all kinds of duplicates removed. Genomes cleanup removed 1277 mouse promoters and 1905 human promoters, and less for other species.
We also added Caenorhabditis elegans (Ensembl release 47) to COTRASIF.
Upon the import of transcripts from Ensembl, and gluing upstream sequences to the first 5'UTR, we ended with exactly duplicated promoters, and also promoters of the different length, which overlap for the full length of the shorter promoter. This duplication lead to multiple duplicates in the results files. This harmless (but annoying) duplication is now partially fixed.
Today we enhanced genome importer to remove promoters derived from the transcripts of the same gene, which are exactly the same. This lead to the noticeable decrease of the numbers of promoters in human (~3400 promoters less), and in mouse (~1000 promoters less). For other species, decrease was less than 300 promoters (in part due to the smaller size of the annotated genes pool).
The problem of overlapping different-length promoters (which also contribute to the duplicate result lines) will be solved soon.
New genome added: Gallus gallus (chicken), Ensembl release 47.
All the species were updated to the latest Ensembl release 47.
Also, we added new organism - Pan troglodytes (chimpanzee).
Name servers of our processing server ceased responding at around 19:00 GMT. We are working to restore functionality, but it will take time to propagate DNS records after the nameserver is accessible again.
Update: normal operations restored at 05:00 GMT on the 26th of October. Total downtime was 10 hours.
We added new organism - Danio rerio (zebrafish).
Now a total of 4 organisms are available - zebrafish, human, mouse, and rat. They will be updated to the latest Ensembl release as soon as one comes out (with a maximum of several days delay).
Until the end of October, we plan extending our database of promoters with at least three more organisms from Ensembl.
The move to the slower server is now cancelled, that we managed to solve instability issues.
We had several long and severe downtimes during the past week. Because of that, we are currently preparing to move to the slower, but much more reliable server (there will be no more "RPC Failed!" error messages). Server move is planned for Sunday, the 14th of October, 2007. During the move, our tools might be briefly unavailable. Sorry for any possible inconveniences.
With the next, 47th release of Ensembl, two genomes - namely human and mouse - will be using ditags for improved UTR prediction. This is expected to considerably increase the quality of the results of COTRASIF for these two organisms.
COTRASIF is launched. It is based on the genomes from now-current Ensembl release 46. We plan to update to the new Ensembl release as soon as one becomes available, which means there can be a 3-5 days delay after new genomes will be in COTRASIF.
Two tools are available at the moment: PWM TFBS finder, and HMM TFBS finder. After additional testing, third tool is planned to be launched today: Conservation filter. Text content (including Help and References) will be added later.
COTRASIF web-interface created.