Hello Zhang, Note the "-" in the summary line in your example:
3 chr21 9885041 9885155 chr12 5667727 5667849 - 771 Alignment coordinates on the negative strand in axt files are given relative to the other end of the chromosome. From http://genome.ucsc.edu/goldenPath/help/axt.html : "Strand (aligning organism) -- 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." So, the so-called "chr12 5667727 5667849" is actually "chr12 5667727 5667849 -", which can be translated to Genome Browser coordinates using the formula described here: http://genome.ucsc.edu/FAQ/FAQdownloads#download20 start = chromSize + 1 - axtEnd end = chromSize + 1 - axtStart For your example, the Genome Browser coordinates would be found like this: mm9 chr12 size: 121,257,530 start = 121,257,531 - 5667849 = 115,589,682 end = 121,257,531 - 5667727 = 115,589,804 You can verify this in the Genome Browser by opening a human (hg18) browser and going to the position chr21:9,885,042-9,885,155, then turning on the Mouse Net track. If you click on the net, you will see this information on the details page: Human position: chr21:9885041-9885155 Mouse position: chr12:115589682-115589804 I hope this is helpful and answers your question. If you have further questions, please feel free to contact us again at [EMAIL PROTECTED] -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/23/08 23:20, zhuqiang zhang wrote: > 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 _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
