31Mr11 2239 I tried to find table browser introduction but got stuck in advance helix (advance table browser; i bounced around the website w/o luck; now try google...putting in "table browser introduction"- just looked; keep going in circles w/o finding introduction (assume it is also dvd like the advanced table browser...will look back through emails and try to find what Mary said- bingo- found the introd dvd cited in Mary's earlier email- have been listening but going to sleep now- like that words and arrows and "print screen" are included- the arrow helps- when I suggested you all publish something to help the naive- this is it and Mary told me, but I didn't begin reading until now- about 2 wks ago when I first googled ucsc genome, I hit one of the main (confusing/busy pages)- would have been useful to see the introd dvd listed (it might have been but the first page was so busy that I didn't notice...anyway...i will examine tomorrow...and remain grateful if anyone has time to help me troubleshoot- i pasted the error message which so far is meaningless to me
((i hope before you post all my emails on your website that you eliminate extraneous/redundant- one reason I wrote so many details was to help you track how a naive/interested/fairlysmart person finds her way through all the words- tough- what helped the most was Mary's email citing all the webpage introd dvds etc A On Thu, Mar 31, 2011 at 9:35 PM, Ann Eileen Miller Baker < [email protected]> wrote: > 1. the below message makes no sense to me > 2. i am examining the USER MANUAL now, but it is LONNNNNG > 3. Mary, perhaps when you help someone so much (you laid/layed out all the > steps), also mention what > sections of the manual are the most important > 4. this is already a very useful website and I hope you all take my > suggestions as you all are > helping me and I am trying to help you improve what is already a useful > resource > > On Thu, Mar 31, 2011 at 9:31 PM, Ann Eileen Miller Baker < > [email protected]> wrote: > >> Can't start query: >> select >> tStart,tEnd,qName,0,strand,tStart,tEnd,blockCount,blockSizes,tStarts,tSize >> from all_sts_primer where tName='chr1' and ((%DMit%)) >> >> --------------------------------------------------------------------------- >> --------------------------------------------------------------------------- >> mySQL error 1064: You have an error in your SQL syntax; check the manual >> that corresponds to your MySQL server version for the right syntax to use >> near '%DMit%))' at line 1 >> --------------------------------------------------------------------------- >> >> >> >> >> >> above is my error message - I got thrown by rexon which I should have >> recognized as UTR exon...but anyway, Mary your >> directions were fairly clear- only the submit is what threw me until my >> husband suggested--- now what to do about error message >> >> QC for you all to think about >> 1. not so bad >> 2. since going back to first page is just mechanical but do zip there, >> perhaps could be >> eliminated? >> 3. since so many hoops to jump through, maybe allow the last submission to >> be saved and then the person >> fixes the goof rather than resubmitting (all those hoops) >> >> I will try to figure out..and hope to get output soon >> Many thanks so far >> A >> >> >> >> On Thu, Mar 31, 2011 at 9:24 PM, Ann Eileen Miller Baker < >> [email protected]> wrote: >> >>> 31Mr11 2132 >>> I called the first one 5'UTRexon >>> that choice is not listed >>> i will try clicking on rexon though that isn't what I typed in >>> >>> On Thu, Mar 31, 2011 at 9:14 PM, Ann Eileen Miller Baker < >>> [email protected]> wrote: >>> >>>> 31Mr11 2112 >>>> 1. I entered 5'UTRexon and hit the button for 5'UTRexon >>>> 2. this caused the computer to go back to page 1 >>>> >>>> On Thu, Mar 31, 2011 at 9:08 PM, Ann Eileen Miller Baker < >>>> [email protected]> wrote: >>>> >>>>> 31Mr31 2107 >>>>> 1. there is no phrase "submit" on page one- I looked 5X; my husband >>>>> looked 2X >>>>> 2. my husband suggested "get output" which led me to next page- is this >>>>> correct? >>>>> >>>>> On Thu, Mar 31, 2011 at 8:50 PM, Ann Eileen Miller Baker < >>>>> [email protected]> wrote: >>>>> >>>>>> 31Mr31 2048 (will work some more; then return here ca. 1500) (thanks >>>>>> to all for your continuing help/patience) >>>>>> (I still feel the PRINT SCREEN combined with arrows would help naive >>>>>> to find places on the fairly busy web page) >>>>>> >>>>>> Vanessa and Mary, >>>>>> 1. I see why on page one I submitted that sequence (see near bottom of >>>>>> page) >>>>>> 2. I am reading Mary's directions for me and see NO PLACE ON PAGE ONE >>>>>> where there is a place >>>>>> to click submit >>>>>> A >>>>>> >>>>>> >>>>>> On Thu, Mar 31, 2011 at 6:08 PM, Ann Eileen Miller Baker < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> 31Mr11 1807 >>>>>>> Vanessa and Mary, >>>>>>> 1. thnx for fast turnaround >>>>>>> 2. Mary (if I understood her) said that those DMit markers >>>>>>> (attached) were part of the UCSC database >>>>>>> 3. the instructions I read said upload- I will reread what Mary wrote >>>>>>> and try again >>>>>>> 4. recall that we need bulk upload/downloads because I have ca. 7500 >>>>>>> DMit loci. >>>>>>> 5. I just got back from my EXCEL/ACCESS tutorial and will be >>>>>>> rereading Mary's directions and then retrying >>>>>>> 6. note each Friday, I am busy until ca. 1500 (EXCEL class) >>>>>>> Respectfully, >>>>>>> A >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Thu, Mar 31, 2011 at 5:21 PM, Vanessa Kirkup Swing < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Hi Ann, >>>>>>>> >>>>>>>> Are you trying to use DMit markers that aren't on the UCSC Genome >>>>>>>> Browser? The instructions below do not ask you to upload a file. Were >>>>>>>> you >>>>>>>> trying to upload a file? >>>>>>>> >>>>>>>> Vanessa Kirkup Swing >>>>>>>> UCSC Genome Bioinformatics Group >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>> From: "Ann Eileen Miller Baker" <[email protected]> >>>>>>>> To: "Mary Goldman" <[email protected]>, [email protected] >>>>>>>> Sent: Thursday, March 31, 2011 12:35:45 PM >>>>>>>> Subject: Re: [Genome] Fwd: pls reply to [email protected] >>>>>>>> >>>>>>>> 31Mr 1235 >>>>>>>> Mary, >>>>>>>> >>>>>>>> 1. I submitted the attached (Witmer DMit for ucsc) >>>>>>>> and got error message >>>>>>>> >>>>>>>> hashMustFindVal: 'hgta_pastedIdentifiers' not found >>>>>>>> >>>>>>>> 2. this was step directly after custom output >>>>>>>> >>>>>>>> 3. I will be here Th until ca. 1500 and return ca. 1700; Friday >>>>>>>> I am in Eureka for ACCESS/EXCEL classes until ca. >>>>>>>> 1500- on most days I am here most of time, just not this Th >>>>>>>> and F >>>>>>>> >>>>>>>> Thanks, >>>>>>>> A >>>>>>>> (I am reading your instructions as I try what you say; i.e., I >>>>>>>> stopped >>>>>>>> reading when I got error message) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Mar 29, 2011 at 4:01 PM, Mary Goldman <[email protected]> >>>>>>>> wrote: >>>>>>>> >>>>>>>> > Hi Ann, >>>>>>>> > >>>>>>>> > I looked at your file and it appears to be a FASTA file of all the >>>>>>>> records >>>>>>>> > from the all_sts_primer table from the mm9 assembly that have >>>>>>>> "D1MIT" in the >>>>>>>> > name. >>>>>>>> > >>>>>>>> > The best way to do this is to A) create a custom track of introns, >>>>>>>> another >>>>>>>> > one of 5' UTR exons, another one of coding exons, etc and B) then >>>>>>>> > sequentially intersect these custom tracks with the all_sts_primer >>>>>>>> table >>>>>>>> > while filtering out the non-DMit records. >>>>>>>> > >>>>>>>> > A) >>>>>>>> > >>>>>>>> > First, let's create a custom track of 5' UTR exons. Go to the >>>>>>>> table browser >>>>>>>> > (http://genome.ucsc.edu/cgi-bin/hgTables) and select the >>>>>>>> following: >>>>>>>> > clade: mammal >>>>>>>> > genome: Mouse >>>>>>>> > assembly: July 2007 (NCBI31/mm9) >>>>>>>> > group: Genes and Gene Prediction Tracks >>>>>>>> > >>>>>>>> > track: UCSC Genes >>>>>>>> > table: knownGene >>>>>>>> > region: genome >>>>>>>> > output format: custom track >>>>>>>> > >>>>>>>> >>>>>>>> >>>>>>>> > >>>>>>>> > and click "submit". On the next page, change the name at the top >>>>>>>> to be >>>>>>>> > something like "5UTRknownGene", choose the "5' UTR exons" button >>>>>>>> and click >>>>>>>> > "get custom track in table browser". >>>>>>>> > >>>>>>>> > Repeat the steps above for introns, coding exons (CDS) and 3' UTR >>>>>>>> Exons. >>>>>>>> > Note that if you choose Exons, this will include both UTR and >>>>>>>> coding exons >>>>>>>> > both. >>>>>>>> > >>>>>>>> > B) >>>>>>>> > >>>>>>>> > Now, go back to the table browser and select the following: >>>>>>>> > clade: mammal >>>>>>>> > genome: Mouse >>>>>>>> > assembly: July 2007 (NCBI31/mm9) >>>>>>>> > group: Mapping and Sequencing Tracks >>>>>>>> > track: STS Markers >>>>>>>> > table: all_sts_primer >>>>>>>> > region: genome >>>>>>>> > >>>>>>>> > filter: click on "create". At the bottom of the page, enter the >>>>>>>> following >>>>>>>> > into the Free-form query section: qName like "%D1MIT%". Click >>>>>>>> "submit". >>>>>>>> > >>>>>>>> > intersection: click on "create". Select: >>>>>>>> > group: Custom Tracks >>>>>>>> > track: 5UTRknownGene (or whatever you named your track in step A) >>>>>>>> > table: there will be only one table so there is no need to select >>>>>>>> one >>>>>>>> > choose: "All all_sts_primer records that have any overlap with >>>>>>>> > 5UTRknownGene" and click "submit" >>>>>>>> > >>>>>>>> > output format: BED - browser extensible data >>>>>>>> > >>>>>>>> > and click "get output". >>>>>>>> > >>>>>>>> > The fourth column should be the names of the DMit loci that are >>>>>>>> located in >>>>>>>> > the 5' UTR. Repeat B for your previously created custom tracks of >>>>>>>> introns, >>>>>>>> > coding exons (CDS) and 3' UTR Exons. Note, that any DMit loci not >>>>>>>> found to >>>>>>>> > be within 5' UTR Exons, introns, coding exons (CDS) or 3' UTR >>>>>>>> Exons are, >>>>>>>> > necessarily, intergenic. >>>>>>>> > >>>>>>>> > I hope this information is helpful. Please feel free to contact >>>>>>>> the mail >>>>>>>> > list again if you require further assistance. >>>>>>>> > >>>>>>>> > Best, >>>>>>>> > Mary >>>>>>>> > ------------------ >>>>>>>> > Mary Goldman >>>>>>>> > UCSC Bioinformatics Group >>>>>>>> > >>>>>>>> > On 3/28/11 6:51 PM, Ann Eileen Miller Baker wrote: >>>>>>>> > >>>>>>>> > 28Mr11 >>>>>>>> > >>>>>>>> > Mary Goldman, >>>>>>>> > Thanks for more details, trying to help me learn enough to >>>>>>>> > find the info I seek. I don't keep the correct email and >>>>>>>> > would be grateful if you forwarded this email to them or whenever >>>>>>>> > you respond you include the correct email and I will forward. >>>>>>>> > Email is fine: I suggested phone because I thought it would >>>>>>>> > be faster. I guess that recombination rates might be guestimated >>>>>>>> > (to an order of magnitude?) with recombinant inbred lines. Any >>>>>>>> > other (indirect way) to guestimate recombination rates >>>>>>>> appreciated. >>>>>>>> > >>>>>>>> > (1a) let me be clearer- the main data I am looking for is >>>>>>>> > ""where mouse usat (microsatellite loci DMit) are located relative >>>>>>>> > to ((regulatory genes (promoters, 5' UTR, intergenes etc and >>>>>>>> > genes (exons)))"" >>>>>>>> > (1b) in brief, I wish to do for mouse usat DMit what Payseur >>>>>>>> > (attachment) did for human usat >>>>>>>> > (2) I have no colleague who refers me to UCSC data on location of >>>>>>>> > usats (microsatellite loci) with respect to regulatory genes >>>>>>>> > (3) I know you are trying to do your best to help me, but can >>>>>>>> > you suggest where I might look to find this information as a file >>>>>>>> > (rather than entering each of the >> 7500 usat individually) >>>>>>>> > (4) I will be looking at wikipedia and the helix websites you >>>>>>>> > suggested asap (in middle of some analyses now, yet wanted >>>>>>>> > to answer your comments, questions as much as I could. >>>>>>>> > (5) How I would like to see output: I WANT TO SEE ALL >>>>>>>> > because I don't know which DMit locus is in exons, introns etc: >>>>>>>> > (5a) DMit locus name >>>>>>>> > (5b) is the DMit locus in an >>>>>>>> > (5b1) exon? >>>>>>>> > (5b2) coding exon? >>>>>>>> > (5b3) intron >>>>>>>> > (5b4) intergene >>>>>>>> > (5b5) 5'UTR (most likely regulatory gene location) >>>>>>>> > (5b6) 3'UTR >>>>>>>> > (5b7) I don't know what cds are (coding?) but will look up in >>>>>>>> > wikipedia/google >>>>>>>> > (5c) These output columns could be summarized as "no evidence >>>>>>>> > for selection (introns)" versus " strong evidence for selection >>>>>>>> (exons >>>>>>>> > in genes important for survival; this would include key promoters >>>>>>>> too)" >>>>>>>> > (6) I have DMit amplified sequences that a colleague sent me >>>>>>>> > (attached)- the DMit name is embedded within a string of other >>>>>>>> > info >>>>>>>> > >>>>>>>> > Mnay thanks for trying to help- we make progress; I will read what >>>>>>>> > you suggested asap. Payseur's paragraph in the MatMeth explains >>>>>>>> > probably more clearly than I can now (still learning). >>>>>>>> > >>>>>>>> > Look forward to hearing from you; will send on to correct email; >>>>>>>> > may write more after reading what you suggested. >>>>>>>> > >>>>>>>> > Ann >>>>>>>> > >>>>>>>> > On Mon, Mar 28, 2011 at 4:55 PM, Mary Goldman <[email protected]> >>>>>>>> wrote: >>>>>>>> > >>>>>>>> >> 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 >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
