Dear Luvina: About one month ago, I asked you about how to find ortholgous site between human and chimpanzee by using human gene coordinates as the query. And you suggest me to use the Batch Coordinate Conversion (liftOver) tools to do the conversion.
It turns out that most the human query have the corresponding site in Chimp. However, the problem is, as my query is gene sequence, and I expect that the converted coordinates in chimp are also locate in generic region. It turns out this is not the case. Here are some of the example: Chimp_chr Chimp_start Chimp_end Chimp_strand Human_chr Human_start Human_end Human_gene Human_strand chr1 16669583 16689734 + chr1 16767166 16786584 NM_018090 + chr1 24989299 25088720 + chr1 25071759 25170815 NM_013943 + When I look these two records of Chimpanzee by using the start and end coordinates in Genome Browser, it turns out they are in the intergenic region. Do you know what could be the possible reason for this? My main purpose is to find the gene coordinates of 1:1 ortholog between human and chimpanzee. Maybe the liftover is not the best tool for this. Do you have any other resource in UCSC browser that I can use? Thank you so much! Best, Jia ----- Original Message ----- From: "Luvina Guruvadoo" <[email protected]> To: "Jia Zeng" <[email protected]> Cc: "genome" <[email protected]>, [email protected], "Soojin Yi" <[email protected]> Sent: Monday, May 9, 2011 12:25:23 PM Subject: Re: [Genome] Question about human and chimpanzee comparative analysis Hi Jia, Alignments between the two genomes are constructed with lastz, formally known at blastz. Please see http://genome.cshlp.org/content/13/1/103.abstract for more information. Also, please see this previously answered question which may be useful for you: https://lists.soe.ucsc.edu/pipermail/genome/2011-May/025889.html --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Zeng, Jia wrote: Hi, Luvina: Thank you for your quick response. It turns out this tool is very helpful to my specific question. I just have one more question. When the liftOver tool perform the coordinates conversion from human genome to the chimpanzee genome, dose it based upon the BLAT alignment, or any other resource? Thanks. Jia ----- Original Message ----- From: "Luvina Guruvadoo" <[email protected]> To: "Jia Zeng" <[email protected]> Cc: "genome" <[email protected]> , [email protected] , "Soojin Yi" <[email protected]> Sent: Friday, May 6, 2011 2:43:50 PM Subject: Re: [Genome] Question about human and chimpanzee comparative analysis Hi Jia, The Batch Coordinate Conversion (liftOver) utility is a useful tool for converting coordinates between assemblies. From the main page, click on 'Utilities' located on the left-side menu, then click on 'Batch Coordinate Conversion (liftOver)'. Here, you can select your original genome/assembly (human/hg18) and new genome/assembly (chimpanzee), and upload your BED file. Once you have submitted your data, scroll down and click on 'View Conversions'. Your results will be displayed in BED format. For general information on how to use the liftOver utility, see: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert . Please feel free to search the Genome mailing list archives by visiting our home page and clicking on "Contact Us" ( http://genome.ucsc.edu/contacts.html ), or email us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Zeng, Jia wrote: <blockquote> To whom it may concern: I would like to use UCSC genome browser to do some comparative analysis between human and chimpanzee. Right now I have the genome coordinates for the region of interest in human (hg18), and I would like to look for the orthologous site in the chimpanzee genome. I have the coordinates in human as BED format, here is the part of the file: chr11 66346610 66346721 3 200 + chr14 90693735 90693787 4 200 + chr3 197937922 197938039 5 200 + chr1 143729237 143729356 6 200 - I wonder if I can directly use this file as an input, and utilize some tool in UCSC genome browser to directly get the coordinates of orthologous site in the chimpanzee. It would be nice if the output file has the same format as my input. Thank you so much and I am looking forward to your reply. Best, Jia Zeng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome </blockquote> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
