Hello again Andrew, Sorry for the delay in answering. Unfortunately, the person here who could best answer your questions is currently unavailable, so we are unable to provide further details. Here is a link to another previous answer that may help: https://lists.soe.ucsc.edu/pipermail/genome/2006-June/010880.html
As for your second question, keep in mind that the axt file format (http://genome.ucsc.edu/goldenPath/help/axt.html) represents alignments on the negative strand differently than the genome browser. From the axt page: "If the strand value is "-", the values of the aligning organism's start and end fields are relative to the reverse-complemented coordinates of its chromosome." We also think that you would benefit from looking at the TransMap track (under Genes and Gene Prediction tracks) since you are looking for syntenic genes between mouse and human. Best, Antonio Coelho UCSC Genome Bioinformatics Group Yi, Andrew wrote: > Thanks for your previous answer, and it is helpful, but here are two more > questions for you: > > 1. > Does syntenicNet/*.hg19.mm9.synNet.axt.gz contain synteny aligments that were > filtered from axtNet/*.hg19.mm9.net.axt.gz? > > Does syntenicNet/*.hg19.mm9.synNet.axt.gz contain all verified synteny > alignments? > but axtNet/*.hg19.mm9.net.axt.gz contain all possible synteny alignments? > > Can you explain what is the syntenic filtering used by UCSC to obtain > *.synNet.axt.gz? > > I opened chr1.hg19.mm9.synNet.axt > Check following records: > HsChr HsAlignStart HsAlignEnd MmChr MmAlignStart MmAlignEnd > MmStrand > chr1 117545799 117546630 chr3 58767584 58768443 > - > chr1 117546643 117546984 chr3 58768741 58769130 > - > chr1 117548413 117549303 chr3 58769477 58770338 > - > chr1 117549304 117549723 chr3 58770744 58771163 > - > chr1 117549800 117549978 chr3 58772957 58773135 > - > chr1 117550280 117550349 chr3 58773136 58773201 > - > chr1 117550350 117550794 chr3 58773387 58773834 > - > chr1 117551098 117553410 chr3 58773836 58775992 > - > chr1 117553464 117555161 chr3 58776218 58777839 > - > chr1 117555330 117555666 chr3 58777843 58778147 > - > chr1 117555689 117557124 chr3 58778236 58779720 > - > chr1 117557125 117557157 chr3 58779846 58779906 > - > chr1 117557158 117559196 chr3 58780060 58782114 > - > chr1 117559493 117559551 chr3 58782115 58782166 > - > chr1 117559552 117561228 chr3 58782343 58784121 > - > chr1 117561229 117561537 chr3 58784243 58784542 > - > chr1 117561570 117561617 chr3 58784564 58784612 > - > chr1 117561618 117562165 chr3 58784984 58785479 > - > chr1 117562204 117562859 chr3 58785792 58786355 > - > chr1 117562866 117562885 chr3 58787836 58787855 > - > chr1 117563203 117563217 chr3 58787856 58787870 > - > chr1 117563218 117563226 chr3 58786356 58786364 > - > chr1 117563227 117563316 chr3 58787880 58787968 > - > chr1 117563324 117563983 chr3 58786365 58786980 > - > chr1 117563984 117564123 chr3 58787177 58787312 > - > chr1 117564139 117565982 chr3 58787510 58789325 > - > chr1 117565997 117566038 chr3 58790824 58790861 > - > chr1 117566339 117566817 chr3 58790862 58791290 > - > chr1 117567152 117567703 chr3 58791291 58791819 > - > chr1 117568022 117568779 chr3 58791820 58792616 > - > chr1 117568780 117569780 chr3 58793550 58794507 > - > chr1 117569819 117570424 chr3 58794833 58795375 > - > chr1 117570743 117571390 chr3 58795376 58795899 > - > chr1 117573139 117574060 chr3 58797339 58798270 > - > chr1 117574215 117574567 chr3 58799130 58799490 > - > chr1 117574568 117574693 chr3 58800084 58800218 > - > chr1 117574694 117577397 chr3 58800336 58802841 > - > chr1 117577398 117578165 chr3 58803250 58803970 > - > chr1 117578476 117578531 chr3 58803976 58804032 > - > chr1 117579311 117579497 chr3 58804568 58804759 > > if I am right, it says human region chr1:117545799-117579497 > match to mouse synteny region chr3:58767584-58804759 > > Am I right? > > 2. however, > When I checked UCSC genome browser > human chr1:117545799-117579497 > turn on only UCSC Gene based on RefSeq, UniProt, ... etc > contain/display: IGSF2 > but after adding comparative genomics tracks > Placental Chain/Net: Full > display Non-primate Placental Mammal Genomes, Chain and net Alignments > Mouse (July 2007 NCBI 37/mm9) Chained Alignments > > display > human IGSF2 at chr1 P13.1 > chr1:117,545,799-117,579,497 > Net map of mouse is > Chr3 - 86799K - 101229K -- 101239K > Mouse Net: chr3 - 100811K > It is not synteny region chr3:58767584-58804759 > > After downloading > hgdownload.cse.ucsc.edu/goldenPath/hg19/database/netMm9.txt.gz > I found out > human chr1:117545799-117579497 > tName:chr1 > tStart-tEnd:117545799-117579497 > match to > mouse records in the qName, qStart and qEnd > chr3 reverse strand 100.8MB > which is consistent with Genme browser result. > > could you please tell which one is correct for human vs mouse synteny gene > translation? > chr1.hg19.mm9.synNet.axt > or > hgdownload.cse.ucsc.edu/goldenPath/hg19/database/netMm9.txt.gz > > thanks for your time > > Andrew > > > -----Original Message----- > From: Antonio Coelho [mailto:[email protected]] > Sent: Thursday, May 06, 2010 1:09 PM > To: Yi, Andrew; [email protected] > Subject: Re: [Genome] source files for synteny regions Q2 > > Hello Andrew, > Since you are looking for synteny information, > syntenicNet/*.hg19.mm9.synNet.axt.gz is most likely what you need, as > they contain the human/mouse alignments after syntenic filtering. If, > however, you are interested in doing your own syntenic filtering, the > axtNet data would more likely suit your needs. > > You can read more about the axt format here: > http://genome.ucsc.edu/goldenPath/help/axt.html > > You should be able to download these files directly form the downloads > page, or through ftp. > > I hope this clears things up. Please feel free to contact us again. > > Antonio Coelho > UCSC Genome Bioinformatics Group > > -------- Original Message -------- > Subject: RE: [Genome] source files for synteny regions Q2 > Date: Thu, 6 May 2010 10:18:06 -0500 > From: Yi, Andrew <[email protected]> > To: Jennifer Jackson <[email protected]> > > Thanks Jennifer, > I visited hgdownload -> human > But I don't need multiple alignments, > Multiple Alignments for 45 genomes: > Multiple alignments of 45 vertebrate genomes with Human > Conservation scores for alignments of 45 vertebrate genomes with Human > Basewise conservation scores (phyloP) of 45 vertebrate genomes with Human > FASTA alignments of 45 vertebrate genomes with Human for CDS regions > > What I need is human (hg19) and mouse (mm9) synteny region translation, > which seems to be > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsMm9/ > > two database files are likely my targets, > axtNet/*.hg19.mm9.net.axt.gz > syntenicNet/*.hg19.mm9.synNet.axt.gz > > but I don't know which one is better? > > > I also visit Utility > Utility descriptions: > http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities > > I did not find any useful information to show me downloading instruction. > > Andrew > > -----Original Message----- > From: Jennifer Jackson [mailto:[email protected]] > Sent: Wednesday, May 05, 2010 1:43 PM > To: Yi, Andrew > Cc: [email protected] > Subject: Re: [Genome] source files for synteny regions > > Hello Andrew, > > The conservation track would be a better choice. Examine the > methods/contents in the browser and then use the Downloads server to > obtain the data. > > For hg19, the data can be found here: > 1) http://hgdownload.cse.ucsc.edu/downloads.html > 2) Human -> Multiple Alignments (four sub-tracks) > > A utility in the kent source tree can help to subset by species: > mafFilter with the option -speciesFilter used. > > Utility descriptions: > http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities > > Pre-compiled: > http://hgdownload.cse.ucsc.edu/admin/exe/ > > Thanks, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/5/10 10:19 AM, Yi, Andrew wrote: > Dear Sir/Madam > > I am looking source files for tables in synteny that contain all > conserved synteny regions (chr and nucleotide sequence locations) > between the genomes of two organisms (human and mouse). > > It seems that both axtNet/*.hg19.mm9.net.axt.gz > and syntenicNet/*.hg19.mm9.synNet.axt.gz > have required info, > e.g. > chr1.hg19.mm9.synNet.axt.txt > 0 chr1 405402 405580 chr1 18566119 18566283 - 3972 > YYI: seems right, but the format very similar to chr1.hg19.mm9.net.axt.txt > 175 chr1 405402 405580 chr1 18566119 18566283 - 3972 > but not all records are identical. > > can you explain why? > and which file is best for my purpose? > > > Andrew > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
