[Genome] A Question regarding the UCSC genome browser

[Ewan Birney]

On 8 Aug 2007, at 17:15, Hiram Clawson wrote:

> Good Morning Oren Ben-Ami:
>
> We only display the strain C57BL/6J
> There are 38 contigs in the 129/SvEvTac strain which you would find
> at NCBI for mouse build 37 (UCSC mm9 under construction).
> You may also be able to find resources at MGI:
> 	http://www.informatics.jax.org/menus/strain_menu.shtml
>

Just to add to this, in a general genomic region we also have some
129 strain information mapped genome-wide at Ensembl;

downloadable at:

ftp://ftp.ensembl.org/pub/current_mus_musculus/data/emf/variation

and viewable graphically in pages like

http://www.ensembl.org/Mus_musculus/transcriptsnpview? 
db=core;transcript=ENSMUST00000003413

In particular the two 129 strains captured genomewide here are:

   129S1/SvImJ and 129X1/SvJ

(I have no idea how close these are to 129/SvEvTac)




> Attached below is a listing of the 38 contigs obtained from the NCBI
> seq_contig.md.gz file:
> ftp://ftp.ncbi.nih.gov/genomes/MapView/Mus_musculus/sequence/BUILD. 
> 37.1/initial_release/seq_contig.md.gz
>
> For mm8 (NCBI build 36) this file would be:
> ftp://ftp.ncbi.nih.gov/genomes/MapView/Mus_musculus/sequence/BUILD. 
> 36.1/initial_release/seq_contig.md.gz
>
> --Hiram
>
> Oren Ben-Ami wrote:
>> Hello,
>> I have a question regarding the mouse genome presented by default  
>> on your
>> Browser. What mouse strain this genome sequence represents? I'm  
>> interesed in
>> the genome sequence of the mouse strain 129/SvEvTac. Is there a  
>> way to
>> configure my UCSC browser to link me to the required genome?
>> I would appreciate a quick response.
>> Best regards,
>>
>> Oren Ben-Ami
>> Dept. of Molecular Genetics
>> The Weizmann Institute of Science
>> Rehovot 76100 Israel
>> Phone: 972-08-9342318
>
>
> chr1 78405337 78677989 NT_039198.1 0 -
> chr1 135130708 135411962 NT_039192.2 0 -
> chr1 175626239 175862001 NT_039194.4 0 -
> chr1 196751751 196918083 NT_165756.1 0 -
> chr10 29215141 29338973 NT_039512.2 0 -
> chr10 74940703 75770483 NT_039510.2 0 -
> chr10 75857962 76062976 NT_039509.1 0 -
> chr10 77365528 77490632 NT_039505.3 0 -
> chr10 77657973 78058093 NT_039514.1 0 +
> chr10 81548321 81740650 NT_096130.1 0 +
> chr11 4576798 4776753 NT_039532.1 0 -
> chr11 4888397 5087722 NT_039536.2 0 -
> chr11 58421679 58592075 NT_078683.1 0 -
> chr11 73788431 73956616 NT_039535.2 0 -
> chr13 107591146 107729579 NT_039594.2 0 +
> chr15_random 1 88442 NT_039622.1 0 0
> chr16 36745476 36789734 NT_097164.1 0 -
> chr16 56599476 56756099 NT_039635.2 0 +
> chr16 94335885 95687261 NT_039634.3 0 +
> chr16 95738235 95953099 NT_165779.1 0 +
> chr17 37435135 38050788 NT_039666.1 0 +
> chr17 46214432 46377798 NT_039670.1 0 +
> chr19 6319225 6451621 NT_039694.4 0 -
> chr19 10118505 10281979 NT_039696.1 0 -
> chr2 20388707 20634820 NT_108908.1 0 +
> chr2 127621298 127781931 NT_039224.2 0 +
> chr3 10755349 10887690 NT_093337.1 0 -
> chr4 143769341 143939932 NT_039291.1 0 +
> chr4_random 1 205573 NT_039289.1 0 0
> chr5 151081772 151546833 NT_039335.1 0 +
> chr5 151674831 151936996 NT_039334.1 0 +
> chr6 15014598 15116520 NT_094805.1 0 -
> chr8 42378189 42561323 NT_039469.1 0 +
> chr8 75584499 75835554 NT_039470.1 0 -
> chr8 77558193 77624349 NT_095755.1 0 -
> chrX 9687416 9797047 NT_039748.1 0 -
> chrX 39214647 39357313 NT_039754.1 0 +
> chrX 40007127 40193888 NT_039738.1 0 +
> chrX 40244235 40330908 NT_039749.1 0 +
> chrX 40330810 40658996 NT_039739.1 0 +
> chrX 68630606 69024237 NT_111918.1 0 +
> chrX 70248991 70372825 NT_099024.1 0 +
> chrX 70626182 71544721 NT_039745.3 0 +
> chrX 71544821 71743246 NT_111917.1 0 +
> chrX 72238442 72736245 NT_039753.2 0 +
> chrX 122946004 123060582 NT_099023.1 0 +
> chrX_random 1 134334 NT_039741.1 0 0
>
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