---------- 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
