Hi Ann, I'm sorry but I've looked again and I can't find data on DMits here. Perhaps your colleague knows which track he used to obtain the data from UCSC?
To better help you there are a couple of things that need to be clarified: 1. Do you have genomic coordinates or sequences? If you are unsure send a small sample in your reply. 2. Specify exactly what loci types are you looking for (intergenic, 3' UTR, CDS, intron or 5'UTR)?. Please note that there is no recombination rate data available for mouse. 3. What are your desired output columns? I'm not sure, but I think they are DMit locus name, DMit sequence and locus type (intron/exon/etc). Before you reply, I highly recommend watching both OpenHelix tutorials below (the first one is about the Genome Browser generally, while the second one focuses on Custom Tracks and the Table Browser, both of which are software features that you will be using): http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml http://www.openhelix.com//cgi/tutorialInfo.cgi?id=28 Additionally, this Wikipedia article may help you understand what we mean by "assembly" here at the Genome Browser: http://en.wikipedia.org/wiki/Genome_project. In particular, this section should help make it clear why there are several assemblies for each organism: http://en.wikipedia.org/wiki/Genome_project#When_is_a_genome_project_finished.3F. Finally, I'm very sorry but we are not funded to provide help via phone. Please reply to the mailing list with any further replies and questions. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 3/22/11 6:14 PM, Ann Eileen Miller Baker wrote: > ---------- Forwarded message ---------- > From: Ann Eileen Miller Baker<[email protected]> > Date: Tue, Mar 22, 2011 at 2:19 PM > Subject: Re: [Genome] pls reply to [email protected] > To: Vanessa Kirkup Swing<[email protected]> > > > 22Mr11 > Dr. Kirkup Swing, > 0. I am asking for more info because now I am reading a study paralleling > my work for which the author made further distinctions than what I > originally requested > 1. thnx- the original DMit amplified sequences came from JAX Informatics; > a colleague sent me the updated sequences which he cited as > coming from UCSC- so your sending me back to JAX (now reproduction > not informatics) seems odd, but I am willing to try to follow your > suggestions > once you respond to my more detailed objectives (below, including ## > annotations within your helpful suggestions## > 2. let me try to be clearer > 3. i have ca. 7500 DMit loci (amplified sequences) for usats > (microsatellites) making it logistically difficult to handle one locus at a > time, which I think > you imply below (these DMit amplification sequences are in your > ucsc mouse DMit usat archive if I understand my colleague) > 4. i am looking for excel files that would have for all DMit usat loci > the location of the amplified loci with respect to the following; i.e., > which > DMit usat loci are in introns? coding exons? etc): > 4a. intron > 4b. exon versus coding exons > 4c. intergenic > 4d. 3' and 5' UTR > 4e. upstream from transcription start site > 5. is there some way to do a "bulk submission" of all these DMit > loci rather than piecemeal (one at a time as I think you imply)? > Ann > ## see below because I don't know what to list for what you > state I need to submit > > On Mon, Mar 21, 2011 at 3:50 PM, Vanessa Kirkup Swing > <[email protected]>wrote: > >> Hi Ann, >> >> Sorry for the delayed response. We suggest you try contacting the mailing >> list (http://reproductivegenomics.jax.org/mailing_list.html) at the >> Jackson Laboratory to see if you can obtain the sequences and positions from >> for the DMit microsatellite markers. >> >> Once you have those, go to the main page on our site. Click on "Tables" >> from the blue navigation bar to get to our table browser. >> >> Set the clade, genome, and assembly. >> > ## what goes into clade? I assume genome implies Mus musculus domesticus; > i don't know what assembly means > ## I need the output to come in excel or text delimited files because I do > the > analyses in EXCEL and in ACCESS; i.e., these formats require a "dedicated" > column for each kind of data > ## my colleague sent me the DMit amplified sequences in FASTA format; > however, since the amplified sequence, has no regular (predictable) > structure, > there is no way to program to get data into "dedicated columns"; i.e., colA > DMit > locus name; colB amplified sequence > > ## may I be sent your phone# so I can try calling if you fail to understand > this? I am usually at 707 786 5342 except for Fridays; this week has an > unpredictable schedule because it is partly a vacation week; otherwise that > phone I will answer > >> Set the following: >> >> track: "UCSC Genes" >> table: "knownGene" >> > ### > ((this is where we need to have bulk submission since I have ca. 7500 DMit > >> region: "position" and click on "define regions." Paste your regions in the >> box and click "submit" >> output format: "all fields from selected table" >> >> click "get output" >> > ## sorry but I am not good at making deductions unless I know well what > I am doing > > exon= expressed gene > intron= where the boundary of the exon is; the intron is outside the exon > boundary > > ## given what I wrote above, how can the pcr silico be of use? > >> The result is the record for your gene. The exon/intron boundaries can be >> deduced from the exonStarts and exonEnds fields. If there are many fields in >> the record that you don't need, you can hit the back button and change the >> output format to "selected fields from primary and related tables." Click >> "get output" and select the fields you wish to see in your results, be sure >> to include exonStarts and exonEnds since these fields contain the data you >> asked about. >> >> Also, you may be interested in UCSC In-Silico PCR for mapping PCR products. >> To get to it, click on "PCR" from the blue navigation bar. >> >> Hope this helps! If you have further questions related to the Genome >> Browser, please contact the mailing list. >> > ## we are further along, but I want to hold off trying to use UCSC (which I > tried > w/o help and got nowhere) but I think you are only giving me > - intron > - exon > whereas I also need > - recombination hotspots > - coding exon versus noncoding exon > - 3' and 5' UTR > - intergenic > >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> ----- Original Message ----- >> From: "Ann Eileen Miller Baker"<[email protected]> >> To: [email protected] >> Sent: Wednesday, March 16, 2011 7:53:57 PM >> Subject: [Genome] pls reply to [email protected] >> >> pls reply to [email protected] because I am unclear how to access >> the >> normal channel where replies are put >> >> (1) How can I find mouse DMit (microsatellite loci) amplified sequences? >> (url) >> (2) alleles at inbred strains for DMit microsatellite loci? (url) >> (3) How can I find which DMit microsatellite loci are in >> - introns >> - exons >> - recombination hot spots >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
