May 2008 - galaxy-user - lists.galaxyproject.org

TFBS search
by Tony Oosterveen 27 May '08

27 May '08

Hello, I am just starting to use galaxy, and I was wondering if there is a simple way to search genome wide for clustering of custom transcription binding sites (preferentially with weight matrixes). All other programs (~10) I have used till so far have their limitations, either the length of the sequence they can handle is rather limited, they use only in house transcription factor binding sites or they are not able to check for evolutionary conservation. Thanks, Tony Tony Oosterveen Karolinska Institute Stockholm Sweden

1 0

Looking For Tool DTD
by Scott Kuehn 24 May '08

24 May '08

Hello, I'm looking for an appropriate DTD to use as a basis for designing new tools (section 3, here: http://g2.trac.bx.psu.edu/wiki/AddToolTutorial) Can someone point me toward this? I looked on the website and the latest source distribution, and could not find anything. Thanks, Scott Scott Kuehn University of Washington Medical Genetics 2211 Elliot: 206-267-1091 x215

2 1

Sharing HIstories?
by Jacob Biesinger 13 May '08

13 May '08

Is it possible to share histories with other collaborators? I'd like them to be able to see my data without having to step through the same steps as I did to generate them. Can this be done in galaxy?

2 1

filter of 3'UTR conserved sequences
by Naum Gershenzon 05 May '08

05 May '08

Dear Sir/Madam, I figured out how to retrieve all conserved human 3'UTR sequences from Table Browser, however they came with multiple repetition (up to 5 times). So my question is “How can I filter these data in order to have all conserved human 3'UTR sequences WITHOUT DUPLICATION THE SAME SEQUEMCES MULTIPLE TIMES?” Sincerely Naum Gershenzon

2 2

feature requests
by Belinda M. Giardine 02 May '08

02 May '08

UCSC Genome Browser output with frame on left with links. Able to upload as custom track at browser of choice eg genome-test or dev browser, watson browser?, ... implemented as url you can point your browser at? Featured datasets eg hard to load dbSNP, too large, keep local? easy access to Ross and other local datasets New Tools To add chr for chroms (Ensembl doesn't include chr) To get uniq rows from a dataset (cat sort uniq) New join choice in Operate on Genomic Intervals -treat interval fields separate so can keep interval file on full join (will work with exact matches to intervals) History - A way of organizing the history into sections/folders, can't just use new histories without reloading core queries, when history is large it is hard to find which query you want when many similar operations done, - A way to archive a history, keep loaded datasets and how to run operations (what was done) but not store all results indefinitely. - When you open a history item could the display not return to the top.

1 0