mouse lemur

[John Alexander]

Dear Sir,

I’m a PhD student in Greece. Had a query on the mouse lemur genome that is available on the browser - even though it seems to displays the latest build for 2007 - it seems to be displaying the 2003 build version. Is there anyway this can be corrected? I’m interested in the conservation, alignment tracks to other species including human,vertebrates, which are available for the latest 2007 mouse lemur build. Please let me know if this can be rectified? Currently I’ve got my data aligned to 2007 build and I’m hesitant to liftOver to 2003. Please let me know if this can be resolved?

cheers,

John Alexander

[Hiram Clawson]

Good Morning John:

It appears our note about a release date of 'June 2003' is incorrect.
The micMur1 UCSC display is the 2007 assembly, there is only one assembly
of this genome sequence:

ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Microcebus_murinus/all_assembly_versions/GCA_000165445.1_ASM16544v1/GCA_000165445.1_ASM16544v1_assembly_report.txt

--Hiram

[Hiram Clawson]

Good Morning John:

We are aware of only one assembly for this genome sequence:
http://www.ncbi.nlm.nih.gov/assembly/GCA_000165445.1

Note the information for this assembly at NCBI:

Date: 2007/07/26
Synonyms: micMur1
Total sequence length 2,902,270,736
Total assembly gap length 1,049,876,375
Gaps between scaffolds 0
Number of scaffolds 185,042
Scaffold N50 140,884
Number of contigs 669,735
Contig N50 3,511
Total number of chromosomes and plasmids 0

The UCSC genome browser displays this NCBI assembly:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=micMur1&chromInfoPage=

contig/scaffold count: 185,042
total size: 2,902,270,736

This does not match the assembly at Ensembl:

Assembly micMur1, Jun 2007
Database version 78.1
Base Pairs 1,852,394,361
Golden Path Length 2,910,103,014

It appears that the assembly displayed at Ensembl is a mixture of the NCBI release
plus the artificial GeneScaffold contigs that the Ensembl gene prediction procedures
construct from the existing scaffolds of the underlying assembly. The UCSC genome
browser hosts the version 78 gene predictions from Ensembl, however the GeneScaffold
coordinates are not used. Ensembl genes that have GeneScaffold coordinates are
partitioned into their separate scaffold units on the UCSC browser display.

--Hiram

On 2/13/15 1:27 AM, John Alexander wrote:
> http://genome-euro.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Mouse+lemur&db=micMur1&position=PSEN1&hgt.positionInput=PSEN1&Submit=submit&hgsid=202532311_pazRvkYYPY9Q9icQarLkNbareZgQ <http://genome-euro.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Mouse+lemur&db=micMur1&position=PSEN1&hgt.positionInput=PSEN1&Submit=submit&hgsid=202532311_pazRvkYYPY9Q9icQarLkNbareZgQ>

[John Alexander]

Dear Hiram,

   Thank you for the prompt response.

Please take a look at the example for PSEN1 gene - the ensembl database is updated with micMur1 july 2007 version:

http://www.ensembl.org/Mouse%20Lemur/Search/Results?q=PSEN1;facet_feature_type=;site=ensembl;facet_species=Mouse%20Lemur

And UCSC brings up:

http://genome-euro.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Mouse+lemur&db=micMur1&position=PSEN1&hgt.positionInput=PSEN1&Submit=submit&hgsid=202532311_pazRvkYYPY9Q9icQarLkNbareZgQ

which I think corresponds to the 2003 version

I think all the alignment files are based on these too - including Human/Mouse lemur : http://hgdownload.cse.ucsc.edu/goldenPath/micMur1/vsHg19/

Even though it says 2007 on clicking http://hgdownload.cse.ucsc.edu/goldenPath/micMur1/vsHg19/ I believe it corresponds to 2003 version. Correct? 

Please let me know.

cheers,

John

[John Alexander]

Sorry also if this is the case - i may want to liftOver between 2007 and 2003 version. I think they liftOver files maybe missing too.

> On 12 Feb 2015, at 18:36, Hiram Clawson <hi...@soe.ucsc.edu> wrote:
>