Feb. 28, 2023

Journal entry homework assignment

For this assignment the UCSC Genome Browser was chosen.

What sort of data is it? What sort of information does it offer us?

The data was initially begun with the Human Genome Project assembly, and has grown since then along with its graphical viewing tool to include many vertebrate and model organism assemblies and annotations. From the home page, we see that there is a species tree from human and its closest genetic relatives in descending order.

When and where was it published? Was it published?

Originally published after the the Human Genome Project completed their first working draft of the human genome assembly, online with a prototype of a graphical viewing tool on July 7, 2000. It has been updated with more genome assemblies and annotations over the years. Citation:

UCSC Genome Browser: Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.

Is this annotation set updated regularly or is it a static source?

The individual human genomes seem to be static sources that are only updated with major versions of data. The previous two as of writing are from Jan. 2022 (T2T-CHM13 v2.0/hs1) and Dec. 2013 (GRCh38/hg38).

Where can I find this data? (link to the download web address or ftp site or publication where it can be found)

https://hgdownload.soe.ucsc.edu/downloads.html

How is the data formatted and released? Does it exist in some sort of standard file format?

Annotation files are available in the bigBed format defined by UCSC, and is advantageous because only the portions of the files that are needed to display a particular region are transferred to the Genome Browser server. The annotation files are also available in .maf (Multiple Alignment Format) and the standard file format .fa (FASTA).

What identifiers are associated with these annotations?

HGNC symbol and UniProt identifiers are amongst those associated with these annotations.