An update to Ensembl release 54 has started

[COTRASIF]

[Bogdan]

Promoters update is now complete, but conservation filter's orthology
mappings are not yet updated.

According to http://www.ensembl.org/info/website/news/index.html :
"Removed the % Identity and % Coverage from the Homolog attributes as
advised by Compara. These are attributes from the WUBLASP step in the
homology inference pipeline but they are not measures of homology
confidence."

Conservation filter relied upon % Identity. Now that it is removed,
I'm looking into using dn/ds values for the same purpose as %id
previously.

Any alternative suggestions are welcome.

[Bogdan]

I've just disabled "Conservation filter" at http://biomed.org.ua/COTRASIF/
to introduce necessary changes after E!54 release.



Also, public genomewide binaries were updated to tolerate non-Ensembl
fasta. However, this is only a quick hack, and "tolerate" is a good
description of it: whenever fasta record has a pipe "|" in it, it is
treated as non-Ensembl; binding sites are found OK, but coordinates
might be totally wrong (no verification has been performed yet, as
this is not an official feature).

I have used these new binaries to calculate some statistics on the
TFBS found in 2nd and 3rd exon sequences with zero cutoff - this
application does not need correct coordinates.

As time permits, support for non-Ensembl fasta will be improved to the
usable level.