[Genome] Re: Update in HMR Conserved Transcription Factor Binding Sites track

[Rachel Harte]

Omer Barad,

Thank you for your compliment on the Genome Browser. There are several
reasons for the differences in this updated HMR Conserved Transcription
Factor Binding Sites track as compared to the hg17 track. The person who
created this track provided me with these reasons roughly in order from
those that made the most difference to those that made the least:

change in minimum threshold (the default threshold for displaying
stayed the same, but the track/table itself now has over 4 times as
many elements)
change in transfac database used
new alignments
new genomes
minor bug in script recently detected that results in some missed hits
(currently being corrected)*
minor alterations to the method

The item marked with an * is being fixed now, so a new version of the
track should hopefully be up in a week or so.

I hope that this answers your question. Please let us know if you have
further questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


> ----- Original Message -----
> From: Omer Barad
> To: genome at soe.ucsc.edu
> Sent: Tuesday, November 14, 2006 1:47 AM
> Subject: Update in HMR Conserved Transcription Factor Binding Sites track
>
>
> Hello,
>
>
>
> Thanks for your great genome browser.
>
> I noticed that you updated the "HMR Conserved Transcription Factor Binding
Sites" track at Nov. 3 2006, the new version contained many changes relative
to the previous version (of May 2004 human genome assembly). Can you say what
caused those changes: is it the updated genome ? the updated conservation
data ? an update in Transfac data ?
>
>
>
> Thanks in advance,
>
> Omer Barad,
>
> Senior scientist,
>
> Rosetta Genomics.
>
>
>
>
>