Hi I am using the method below to fetch orthologous coding regions. When I define a region I use the coordinates from ensembl. In most cases the coordinates agree but in some cases they are different in UCSC. Is their a way to by pass this problem. Can I download the coordinates of the Ensembl genes as they are in UCSC..
Thank you Nicholas On 20 January 2011 17:23, Vanessa Kirkup Swing <[email protected]> wrote: > Dear Nicholas, > > Now that we know that you are looking for the orthologous protein coding > regions, there is a great tool in the table browser > (http://genome.ucsc.edu/cgi-bin/hgTables) to do this. > > Please set the following: > > genome: Human > assembly: hg19 > group: Genes and Gene Prediction tracks > track: Ensembl Genes > table: ensGene > region: click "define regions" and paste in your coordinates. > output file: CDS FASTA alignment from multiple alignment (this will get you > the orthologous protein coding regions) > > and click "get output". > > click the "+" button next to the primate to select all of the primates or > you can select the individual primates that you are interested in. > Note: There are formatting options at the top of this page that might be of > interest to you. > > click "get output". > > > Hope this helps! > > Vanessa Kirkup Swing > > > ----- Original Message ----- > From: "Nicholas Price" <[email protected]> > To: [email protected] > Sent: Thursday, January 20, 2011 9:14:39 AM > Subject: Re: [Genome] Intron-removal > > Hi > > I am trying to find orthologous protein coding regions in primates. I have > the coordinates of the Ensembl genes, however these coordinates include > introns and exons. SO when I use them the way you suggested below I will get > alignments that include exons and introns..SO I am trying to find a way to > get the only the protein coding part. For example a way that I could do it > is to get the coordinates of the exons that make the protein coding part of > the gene and then use multiz46 to get the orthologous regions....and in the > end concatenate them together.....However I am worried that the exon parts > are too small and may get ambiguous results. Is there another way which is > better??? I hope I am clearer this time.. > > Nicholas > > > > On 21 December 2010 16:54, Mary Goldman <[email protected]> wrote: > >> Hi Nicolas, >> >> I think I may not be fully understanding what you are asking. The way I >> read your question is that you have the coordinates of one human gene for >> which you are trying to find the primate ortholog using the Conservation >> track. You want only the coding region for this gene. If this is the case >> you can do the following using the Table Browser: >> >> genome: Human >> assembly: hg19 >> group: Comparative Genomics >> track: Conservation >> table: Multiz Align (multiz46way) >> region: click "define regions" and paste in your coordinates. >> intersection: click "create". Choose a gene prediction track and choose >> the radio button " All multiz46way records that have any overlap with >> 'gene prediction track'". Click "submit". >> output file: enter a name if you want to save the output as a file >> >> and click "get output". >> >> I'm sorry if I am not completely understanding your issue. Please send some >> clarifying information to the list if this does not resolve your issue (I >> may not be available due to the holidays - that is why it would be best if >> you could send it to the list). >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> ----- Original Message ----- >> From: "Nicholas Price" <[email protected]> >> To: "Mary Goldman" <[email protected]> >> Sent: Tuesday, December 21, 2010 1:10:29 PM >> Subject: Re: [Genome] Intron-removal >> >> Hi Mary >> >> >> I want to confirm that the answer you send me below is for getting >> orthologous pseudogenes and not on how to remove intronic regions >> >> >> Nicholas >> >> >> >> On 21 December 2010 13:45, Mary Goldman < [email protected] > wrote: >> >> >> Hi Nicolas, >> >> We recommend following the steps in this previous mailing list question: >> https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024414.html , >> except that when you create an intersection with your gene track of >> interest, choose "Base-pair-wise intersection" or "All Mulitz records that >> have any overlap ..." . >> >> 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 >> >> >> >> >> ----- Original Message ----- >> From: "Nicholas Price" < [email protected] > >> To: [email protected] >> Sent: Tuesday, December 21, 2010 10:32:50 AM >> Subject: [Genome] Intron-removal >> >> Hi >> >> I want to find all the primate orthologs to a Human gene and retrieve only >> the coding region. I use the Human Genome, conservation track, comparative >> genomics, Multiz-Align. I put the coordinates of my gene..and I retrieve >> the >> alignments. I do all this from a perl script..I am wondering how to filter >> out the intronic regions ..etc and get only the coding region? Is there an >> option in Tables that does that? >> >> >> Nicholas >> -- >> The oppressed become the oppressors Paulo Freire (1921-1997) >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> >> -- >> The oppressed become the oppressors Paulo Freire (1921-1997) >> > > > > -- > The oppressed become the oppressors Paulo Freire (1921-1997) > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- The oppressed become the oppressors Paulo Freire (1921-1997) _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
