Joseph, Thanks for your reply. I am familiar with BLAT. I did all you described to find the orthologous soy data. I routinely use the soybase interface for that.
What we would like to do is zoom in on the Pv sequences at or nearby the loci for rust resistance. What we did is: type rust for the markers. export the CSV file see excel attach blast 3 scar sequences which are known to the soy data in the browser and in soybase/ncbi _result only ~5% of fragments give good alignment at few different loci> ALL the SCAR sequences do not have orthologous sequences in Gmax! So for all rust marker sequences there is no ortholog in Gmax? I find that hard to believe. It means we cannot access Pv alignments through the Gmax built? I also attached a picture of the browser highlighting some Pv tracks (abi). How do we extract those sequences? Is there a mirror location for ftp somewhere? PLease feel free to comment. Kind regards Vriendelijke groeten -john ----- Original Message ----- From: Joseph Fass To: Paul Gepts Cc: GreenAcres ; Dawei Lin Sent: Thursday, February 16, 2012 5:47 PM Subject: Re: Fw: [Genome] use of gmax and Pv assemblies Hi Mr. Groenendijk, I could add that BLAT is very similar to BLAST, and is used on the UCSC site mainly for speed / computational reasons. Blasting the markers in the PhaseolusGenes database (using the link below the sequence) to soybean, or using the pre-computed AB-Blast results at the top of the marker's page (when they exist), should find the orthologous soybean sequence. You could further tune your BLASTs by copying the sequence of the marker to NCBI's or Phytozome's BLAST interface, and specifying soybean as the target. Hope that helps, ~Joe On Thu, Feb 16, 2012 at 12:52 AM, Paul Gepts <[email protected]> wrote: Dear Mr. Groenendijk, Thank you for your inquiry into the functionalities of the PhaseolusGenes database. In order to fully understand your question, could you please explain what your goal is. Would you like to identify additional sequences linked to existing SCAR markers? Best, Paul Gepts 2012/2/16 GreenAcres <[email protected]> Dear Dr. Lin, Dear madam, sir, After attending the BIC-meeting late 2011 we would like to use the phaseolusgenes site for making amplicons in regions of interest to test in our own breeding material. The site is linked to the glycine max built and the Phaseolus alignments is one of the tracks. We would like to look at regions with rust resistance genes. !@ sequences appear in the phaseolusgenes. It is not clear how we can relate these to their map location in the G.max genome browser since there is no blat function. What would be the best way to proceed? Do we need to download the G.max or Pv. scaffolds ourselves? I hope you can be of help. I will attach a list of known scar markers for rust resistance. Sincerely and kind regards, John Groenendijk Wageningen University/Greenacres. ----- Original Message ----- From: "Steve Heitner" <[email protected]> To: <[email protected]>; <[email protected]> Sent: Wednesday, February 15, 2012 8:05 PM Subject: RE: [Genome] use of gmax and Pv assemblies Hello, John. I believe you are referring to this site: http://phaseolusgenes.bioinformatics.ucdavis.edu/. If that is correct, you will find the appropriate contact information at the bottom right corner of that page. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Wednesday, February 15, 2012 7:38 AM To: [email protected] Subject: [Genome] use of gmax and Pv assemblies Importance: High Dear madam, sir, After attending the BIC-meeting late 2011 we would like to use the phaseolusgenes site for making amplicons in regions of interest to test in our own breeding material. The site is linked to the glycine max built and the Phaseolus alignments is one of the tracks. We would like to look at regions with rust resistance genes. !@ sequences appear in the phaseolusgenes. It is not clear how we can relate these to their map location in the G.max genome browser since there is no blat function. What would be the best way to proceed? Do we need to download the G.max or Pv. scaffolds ourselves? I hope you can be of help. I will attach a list of known scar markers for rust resistance. Sincerely and kind regards, John Groenendijk Wageningen University/Greenacres. -- ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ Prof. Paul Gepts University of California Department of Plant Sciences / MS1 Section of Crop and Ecosystem Sciences 1 Shields Avenue Davis, CA 95616-8780 Tel: +1-530-752-7743 Fax: +1-530-752-4361 Web: http://www.plantsciences.ucdavis.edu/gepts/geptslab.htm ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ -- Joseph Fass Lead Data Analyst UC Davis Bioinformatics Core joseph.fass -at- gmail.com (professional) 970.227.5928 (c) || 530.752.2698 (w)
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