Dear all, sorry if I am doing a very silly mistake somewhere... I want to retrieve the MAOA sequences for the primates, mouse and rat. Human and rodents are all right, but it seems that the primate sequences are not available since I am getting only non-Rhesus RefSeq genes and such.
What is wrong? Please, advise! sincerely, elena shumay -----Original Message----- From: [email protected] on behalf of [email protected] Sent: Wed 12/7/2011 5:43 PM To: [email protected] Subject: Genome Digest, Vol 107, Issue 17 Send Genome mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.soe.ucsc.edu/mailman/listinfo/genome or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Genome digest..." Today's Topics: 1. gorilla genome liftover tools... (Woerner, August E - (augustw)) 2. Re: Local mirroring issues with compiled cgi-bin (Greg Roe) 3. Re: Isoform prediction (Vanessa Kirkup Swing) 4. Re: How the chromosomes with 2L and 2R are aligned (Fahim Mohammad) 5. repbase version info? (Janet Young) 6. a question of finding overlap (Zhi Zhang) 7. Re: first intron, first coding exon from table browswer output (Vanessa Kirkup Swing) ---------------------------------------------------------------------- Message: 1 Date: Wed, 7 Dec 2011 11:35:24 -0800 From: "Woerner, August E - (augustw)" <[email protected]> Subject: [Genome] gorilla genome liftover tools... To: "[email protected]" <[email protected]> Message-ID: <E03D709415B0584FA795B53609BB09AF0A423B628D@VA3DIAXVS691.RED001.local> Content-Type: text/plain; charset="us-ascii" Hi! I am interested in relating information mapped to gorGor3 to gorGor3.1. What is the best way to go about this? I realize that liftOver would be a great solution to this problem, but I doubt that many other people would have need of this particular conversion. What would you suggest I do? I would be more than happy to generate the liftover files myself, if someone could give me a protocol for doing so. Much thanks! -August PS On a completely unrelated note, the sex-averaged recombination rate data for the human X chromosome is a little... wrong, on this site. I tried alerting UCSC to this fact many years ago, and nothing ever happened. It's not your fault, mind you-- it's the table itself that has the wrong information. The short of it is that the population sex-averaged recombination rate of the X is 2/3 of the female rate (ignoring the parts of the X that recombine w/ the Y), and, if memory serves, the rate that shows up as the "sex-averaged" value is the female value (sometimes... I think in some of the maps it's 1/2 the female rate). Regardless, correcting these tables might help those of us that study the X! Thanks again! And I love your site! ------------------------------ Message: 2 Date: Wed, 07 Dec 2011 12:21:25 -0800 From: Greg Roe <[email protected]> Subject: Re: [Genome] Local mirroring issues with compiled cgi-bin To: Devasta Palle <[email protected]> Cc: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Devasta, We have not tested on 32-bit machines in quite some time, so we can't say for sure if that might be an issue. As far as the segmentation fault error - you might try debugging with JKSQL_TRACE=on in the URL or with 'strace -f', which may give you an idea of where it's stopping. See this previous mailing list question for some additional info: https://lists.soe.ucsc.edu/pipermail/genome-mirror/2011-September/002831.html Also see this wiki entry: http://genomewiki.ucsc.edu/index.php/Browser_Installation#If_it_doesn.27t_work... The database setup can lead to segmentation faults if tables are missing or hgcentral is not correct. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 12/3/11 9:11 AM, Devasta Palle wrote: > Hi all, > > I am on a 32-bit debian 6 machine. > I compiled the CGIs of the jksrc and, after a minimal set up of mysql > database and hg.conf, I tried to run some of the CGI binaries from the > command line. > hgTables gives me a Segmentation Fault error after printing the following > line: > > Set-Cookie: hguid=106; path=/; domain=; expires=Thu, 31-Dec-2037 23:59:59 > GMT > > Besides, the output (HTML) of hgTracks is much less of that of the webpage > at genome.ucsc.edu/cgi-bin/hgTracks. > > My goal is to set up a genome browser mirror (for few species) with at > least hgTracks and hgTables functionality. > > Has anyone had similar issues and solved them? > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome ------------------------------ Message: 3 Date: Wed, 7 Dec 2011 12:41:19 -0800 From: Vanessa Kirkup Swing <[email protected]> Subject: Re: [Genome] Isoform prediction To: "Mercer C.L." <[email protected]> Cc: "[email protected]" <[email protected]> Message-ID: <capbuke58tdwknymbu8eqau1hfg5223qcwgf7434cb7goc6m...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Catherine, We recommend that you take a look at the description page for the track that you are interested in. Track description pages are accessible from the Genome Browser by clicking the links above the visibility settings. Here is an example of a track description page for the RefSeq Genes track in the hg19 assembly: http://genome.ucsc.edu/cgi-bin/hgTrackUi?DB=hg19&c=chr10&g=refGene Please note that some gene tracks are the result of manual curation while others are the result of predictions. We hope this helps lead you in the right direction. If you have further questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Mercer C.L. <[email protected]> Date: Tue, Dec 6, 2011 at 5:09 AM Subject: [Genome] Isoform prediction To: "[email protected]" <[email protected]> Dear UCSC colleagues Is there a way of knowing how the isoforms that are listed for a particular gene have been generated? Is it clear if they are a result of insilico predictions using ESTs or if the information comes from actual experimental data? Thank you Best wishes Catherine Catherine Mercer School of Medicine University of Southampton Centre for Human Development, Stem Cells and Regeneration Human Genetics The Duthie Building (MP808) Southampton General Hospital Tremona Road Southampton SO16 6YD _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome ------------------------------ Message: 4 Date: Wed, 7 Dec 2011 16:06:13 -0500 From: Fahim Mohammad <[email protected]> Subject: Re: [Genome] How the chromosomes with 2L and 2R are aligned To: Vanessa Kirkup Swing <[email protected]> Cc: [email protected] Message-ID: <CANf0P=+NUQL=qkckeb-jh4v3eewpezowljb4phhh0yc5m+t...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Thanks for reply. I am interested in finding the annotation of gene symbol on the Anopheles Gambaie Genome. Is there a table or annotation file from which I can somehow know the start and end position of a gene on this genome. There is a table named 'geneName.txt.gz' on http://hgdownload.cse.ucsc.edu/goldenPath/anoGam1/database/ and the entries are as follows 0 n/a 2299 1 thrB 10010 2 argA 8888 3 sam-pr 151442 4 hacA 9034 5 nifH 9589 6 azr 2487 7 LipL32 113812 The first column is ID, second is the geneSymbol and third is CRC. For other organisms there are Refseq files and from there I can get the coordinate information for gene symbols. But AnoGam1 does not have that file. Is there any other way to find BED files for these gene symbols or at least the start and end location of these genes. Thanks Fahim On Wed, Dec 7, 2011 at 2:13 PM, Vanessa Kirkup Swing <[email protected]>wrote: > Hi Fahim, > > We looked into your issue and we suspect that there is an issue with NCBI > and we suggest that you contact them. > > If you have further questions, please contact the mailing list: > [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > ---------- Forwarded message ---------- > From: Fahim Mohammad <[email protected]> > Date: Tue, Dec 6, 2011 at 3:52 PM > Subject: [Genome] How the chromosomes with 2L and 2R are aligned > To: [email protected] > > > Hi > I am working on Anopheles Gambiae genome and I am facing problem when > comparing the result from NCBI and genome browser. > The chromosome names at UCSC browser that AnoGam1 have are chr 2L, 2R, 3L, > 3R, X and Un where as NCBI somehow combine L and R files together to get > one genome. > > Is there a way to make the data from UCSC and NCBI such that the chromosome > nomenclature as well as the coordinates becomes similar. > > Thanks > Fahim > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > -- ------------------------------- Fahim Mohammad Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167 web: http://bioinformatics.louisville.edu/lab/ ------------------------------- I think the reason people are dealing with science less well now than 50 years ago is that it has become so complicated. --James D. Watson<http://www.brainyquote.com/quotes/quotes/j/jamesdwat388959.html> ------------------------------ Message: 5 Date: Wed, 7 Dec 2011 13:01:55 -0800 From: Janet Young <[email protected]> Subject: [Genome] repbase version info? To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=us-ascii Hi there, I'm looking for information on which version of RepBase was used to produce the rmskRM327 track for hg18? (I see that info for the rmsk track, but not the rmskRM327 track). Apologies if this has been asked before: I see a version of the question for other assembly versions, but not this one. thanks very much, Janet Young Fred Hutchinson Cancer Research Center ------------------------------ Message: 6 Date: Wed, 7 Dec 2011 13:11:08 -0800 From: Zhi Zhang <[email protected]> Subject: [Genome] a question of finding overlap To: "[email protected]" <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" Hi, All, I have some SNP position data in dm3 and want to find whether they are in 5kb upstream region in dm3 genome. how can I do that in table search of UCSC? THANKS Zhi Zhang, Ph. D. Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Rd. La Jolla, CA 92037, USA Phone 858-646-3100 ext. 3801 Fax 858-795-5298 ------------------------------ Message: 7 Date: Wed, 7 Dec 2011 14:43:25 -0800 From: Vanessa Kirkup Swing <[email protected]> Subject: Re: [Genome] first intron, first coding exon from table browswer output To: Ann Eileen Miller Baker <[email protected]> Cc: [email protected] Message-ID: <CAPBuKE4SigHz_F3HkdT8Dwv+u1-B=u6ut7n90swoodyvcx_...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Ann, All of the necessary information is in the table browser output. If you have lost information when copying over the data to excel, we suggest that you go through and do the steps again and use to the table browser output to do your analysis. We are unable to assist you with putting the table browser output into excel format. If you have further questions about the UCSC Genome Browser, please email: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Ann Eileen Miller Baker <[email protected]> Date: Tue, Dec 6, 2011 at 3:08 PM Subject: [Genome] first intron, first coding exon from table browswer output To: [email protected] 6Dc11 Genome team, Thanks for coaching Brooke. Below continues the question about recognizing the first intron and first coding exon. Rather than keep "print screen" of the TABLE BROWSER output, I copied from TABLE BROWSER and pasted into EXCEL files (attached). This means I have no data pertinent to "CDS exons" or the "_0". The attached files (coding exon; intron) show that nearly all DMIT loci are listed ONCE, which if I understand from Brooke to mean that all these loci are the FIRST CODING EXON or FIRST INTRON. Is using my files (attached) OK to show that most DMIT loci are in first intron or first coding exon? Or should I go back to the TABLE BROWSER and request again introns or coding exons so I can the "_0" and the "(uc002yow.1)" Look forward to hearing from you, Ann _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome ------------------------------ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome End of Genome Digest, Vol 107, Issue 17 ***************************************
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