Microcebus murinus annotation

Camille Ezran

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May 5, 2016, 1:39:12 PM5/5/16

to gen...@soe.ucsc.edu

Hi,

I am a researcher at Stanford University studying mouse lemurs (Microcebus murinus). I would like to know more about the UCSC microcebus annotation. According to the website, the UCSC genome browser assembly was released in May 2015. However, when I browse for specific genes there are only non-microcebus refseq genes that come up. This is surprising to me since the NCBI refseq annotation was also released recently. Is there a reason the refseq genes do not appear in the search? How can I have access to the mouse lemur transcripts in order to align them with transcripts from other primates?

Thank you,

Camille Ezran

Brian Lee

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May 9, 2016, 7:59:40 PM5/9/16

to Camille Ezran, gen...@soe.ucsc.edu

Hello Camille,

Thank you for using the UCSC Genome Browser and for submitting your question regarding learning more about the UCSC mouse lemurs (Microcebus murinus) annotation.

On our public site we do not have this additional information, but you might be interested in investigating our prototype work-in-progress pipeline assembly hub: http://genome-preview.cse.ucsc.edu/gbdb/hubs/genbank/vertebrate_mammalian/vertebrate_mammalian.ncbi.html

This assembly hub includes an entry for GenBank assembly accession GCA_000165445.2/ RefSeq assembly accession GCF_000165445.1, where you can find some RefSeq Predictions:
http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://genome-preview.cse.ucsc.edu/gbdb/hubs/refseq/vertebrate_mammalian/hub.ncbi.txt&genome=GCF_000165445.1_Mmur_2.0&position=lastDbPos

Click into "ncbiGene" track and see the line explaining The NCBI Gene track is constructed from the gff file GCF_000165445.1_Mmur_2.0_genomic.gff.gz delivered with the NCBI RefSeq genome assemblies at the FTP location: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000165445.1_Mmur_2.0

Also on our preview site on the micMur2 browser, http://genome-preview.cse.ucsc.edu/cgi-bin/hgGateway?db=micMur2, we have a track that displays NCBI RefSeq predictions. Most of the gene predictions here should be correct, but some of them may not be as they are not curated: http://genome-preview.cse.ucsc.edu/cgi-bin/hgTrackUi?db=micMur2&g=refSeqComposite

Please keep in mind that this is our preview instance and has software and data that can change at any time as there are items that have yet to go through our QA process before release to our public site.

Also of importance is to note that some of the genes in these tracks may not be correct depending upon issues in the NCBI prediction system or the translation procedures taking place to load the data on our preview site. We have been thinking about how to verify this NCBI RefSeq gene track, all the genes in this track are predictions from the NCBI procedures and none of these genes are 'curated'. Our engineers highly suggest if you use this data to verify any notations that are critical to your work.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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Camille Ezran

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May 12, 2016, 6:52:49 PM5/12/16

to Brian Lee, gen...@soe.ucsc.edu

Hi Brian,

Thank you for your reply. The links to the the preview website and refseq predictions are very helpful! We look forward to seeing the mouse lemur genome on the UCSC public site soon.