Hi Nicholas, Please see the Conservation track description page, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way, for more information about mutliz.
Katrina Learned UCSC Genome Bioinformatics Group Nicholas Price wrote, On 01/21/11 14:24: > 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 >> >> > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
