h19 genome assembly

[Li FAN]

Hi Team,

I am a neuroscientist in Wisconsin.

Could you please help me to answer following questions on genome assembly?

(1) How did you build genome assembly hg19?

 

(2) Do you combine RefSeq (NM_xxxxx) from Genebank with other intronic sequences into a genome assembly hg 19?

 

or (3) Do you assembly genome hg 19 from raw data from completely different research projects without including RefSeq from GeneBank?

(4) How did you build genome assembly for hg 38?

Thank you very much!!!

Li

[Brian Lee]

Dear Li,

Thank you for using the UCSC Genome Browser and your question about the human genome assembly.

While the UCSC Genome Browser displays assemblies, most often it is consortiums that work to sequence and assembly the final genomes and then we simply display that information. All of your human genome assembly questions (hg19=GRCh37 and hg38=GRCh38) should be directed to the Genome Reference Consortium (GRC) in connection with the National Center for Biotechnology Information (NCBI).

NCBI and the GRC have extensive amounts of information to help you learn about the human assembly, from introductory overviews of the process, to links that will provide you very detailed information (and raw data). Here are some links to start you off:
https://www.ncbi.nlm.nih.gov/grc/data
https://support.ncbi.nlm.nih.gov/link/portal/28045/28049/Article/752/How-are-genome-assemblies-generated-and-what-are-assembly-levels
https://www.ncbi.nlm.nih.gov/assembly/basics/

Your questions about RefSeq and GenBank data likely indicate you may be interested in the Gene Prediction process, but these questions are not really about genome assembly. Gene Prediction is a secondary stop to constructing an assembly for an organism and part of annotating experimental data onto the genome or analyzing the genome sequence to make predictions. Once you review the materials at NCBI these secondary questions will be contextualized.

Lastly you may be interested in our training page, http://genome.ucsc.edu/training/index.html, that provides links to resources and videos about using the Browser.

Thank you again for your writing to us 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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