In addition, please look at the webpage: http://genome.ucsc.edu/cgi-bin/hgc?hgsid=116366124&o=9885041&t=9885155&g=netMm9&i=1&c=chr21&l=9885041&r=9885155&db=hg18&pix=1200
The location showd on that page is correct.(the same with blat) But it is different in archived file: chr21.hg18.mm9.net.axt.gz Would you lease check it for me? Thanks you very much. 2008/11/24 zhuqiang zhang <[EMAIL PROTECTED]>: > Dear Zweig: > > You may have misunderstood my meaning. Let's still look at the example > block from hg18/mm9 blastz alignment: > > 3 chr21 9885041 9885155 chr12 5667727 5667849 - 771 > GGTCAAGTAACTGAGGACAAGGATCAATAGAAACAAGGACACACTCTAATTTTATGATAAATATTTTATTCAAGAGTCACCGTATACAGAAAATTCAAAG---------------ATTAGTAAAGGCCCt > GATTAAATCATTAAGGA-AGGGAATAAAAACACTATGAACTCATTC---TCTTTTAATTGGTAATTTTCCCAA---TCGCTCTTCATGCAAGATGTAGAGTGAAGGGCCCTCTCAGTTAGTAAAGCTTTT > > As we can see, the latter seq are from so-called "chr12 5667727 > 5667849".I retrieved the seq of that genomic region. But it is totally > different at all. I believe the number of the 2nd genome is wrong. It > is unrelated to Blat. > > Thanks for your patience. > Best regards, > Zhuqiang, Zhang. > > 2008/11/22 Ann Zweig <[EMAIL PROTECTED]>: >> Hello Zhang, >> >> The files that you are looking at are not created by >> BLATting one genome against the other one. They are created >> using a series of algorithms and software. They are the >> basis for the Chain and Net annotation tracks in the browser. >> >> Here is a brief explanation of the methods used, from the >> description page of the Chain track: >> >> Transposons that have been inserted since the human/mouse >> split were removed from the assemblies. The abbreviated >> genomes were aligned with blastz, and the transposons were >> added back in. The resulting alignments were converted into >> axt format using the lavToAxt program. The axt alignments >> were fed into axtChain, which organizes all alignments >> between a single human chromosome and a single mouse >> chromosome into a group and creates a kd-tree out of the >> gapless subsections (blocks) of the alignments. A dynamic >> program was then run over the kd-trees to find the maximally >> scoring chains of these blocks. >> >> Consequently, I would not expect the alignments in the file >> to exactly match the BLAT results. >> >> For more details on the blastz program, you can read this >> paper: http://pipmaker.bx.psu.edu/dist/blastz.pdf >> >> Regards, >> >> ---------- >> Ann Zweig >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> >> >> zhuqiang zhang wrote: >>> Dear Zweig： >>> >>> sorry， I used the wrong example. It is from the hg18/vsMm9 >>> file: chr21.hg18.mm9.net.axt.gz . >>> >>> But the 2nd seq is at mm9 chr12:115589682-115589804 (BLAT >>> result), NOT chr12:5667727-5667849. So, it still puzzles me. >>> >>> Best regards; >>> ------------------------- >>> Zhuqiang, Zhang >>> >>> >>> 2008/11/21 Ann Zweig <[EMAIL PROTECTED]>: >>>> Hello Zhang, >>>> >>>> It looks like you may be looking at the wrong file. The snippet you >>>> provide below is from the file located in the hg18 directory here: >>>> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsMm9/axtNet/ >>>> >>>> That is, the human assembly (hg18) is listed first, and mouse (mm9) >>>> is listed next. I can tell this is so, because the mouse does not have 21 >>>> chromosomes. This should explain the discrepancy you are seeing. If you >>>> look at the file with this new information in mind and you are still not >>>> able to understand it, please feel free to write back to the list. >>>> >>>> >>>> Regards, >>>> >>>> ---------- >>>> Ann Zweig >>>> UCSC Genome Bioinformatics Group >>>> http://genome.ucsc.edu >>>> >>>> Please feel free to search the Genome mailing list archives by visiting our >>>> home page, clicking on "Contact Us", then typing a word or phrase into the >>>> search box. On that same page >>>> (http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome >>>> mailing list. >>>> >>>> >>>> >>>> >>>> zhuqiang zhang wrote: >>>>> Dear sir: >>>>> I downloaded the blastz result of mm9 vs hg18 from >>>>> http://hgdownload.cse.ucsc.edu/goldenPath/mm9/vsHg18/axtNet/ . But I >>>>> found the location numbers of hg seqs in those files are strange. >>>>> For example: >>>>> >>>>> 3 chr21 9885041 9885155 chr12 5667727 5667849 - 771 >>>>> >>>>> GGTCAAGTAACTGAGGACAAGGATCAATAGAAACAAGGACACACTCTAATTTTATGATAAATATTTTATTCAAGAGTCACCGTATACAGAAAATTCAAAG---------------ATTAGTAAAGGCCCt >>>>> >>>>> GATTAAATCATTAAGGA-AGGGAATAAAAACACTATGAACTCATTC---TCTTTTAATTGGTAATTTTCCCAA---TCGCTCTTCATGCAAGATGTAGAGTGAAGGGCCCTCTCAGTTAGTAAAGCTTTT >>>>> >>>>> As described, the human seq block is located at "chr12 5667727 >>>>> 5667849"; But in fact, the latter sequence is at >>>>> "chr1:42836935-42836958". You can confirm that with Blat tools. >>>>> >>>>> Thank you! I appreciate your time very much! >>>>> >>>>> Zhuqiang, Zhang >>>>> Institute of Zoology, CAS, Beijing >>>>> _______________________________________________ >>>>> Genome maillist - [email protected] >>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
