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
>
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>
>
>
> 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
>
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