Thank you very much for the reply-) One more question. From what I understand multiz is used to identify orthologous regions?. So for example if I am looking for orthologs in primates for a gene that is found only in Human, is multiz suppose to return no output or will return any region that has homology?
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
