Genomika: Rozvojové projekty

MalGlo group

User trackDb, code management

• Think how to better manage changes to browser code in the future instances of the course
• Explore possibilities of each user having their own trackDb
• Start by reading short info in /kentsrc/trackDb/makefile on genomika server

# Browser supports multiple trackDb's so that individual developers
# can change things rapidly without stepping on other people's toes. 
...

• Write a manual how to do your suggested changes and test it

Rfam

• Rfam http://rfam.xfam.org/ is a database of families of non-coding RNAs
• It contains a covariance model for each family
• The database can be downloaded and searched against a genome using Infernal tool http://eddylab.org/infernal/
• Do this search, then convert the output to appropriate format and display in the browser
• Possibly use BEDdetail format https://genome.ucsc.edu/FAQ/FAQformat.html#format1.7
• After clicking on an Rfam match, there should be some display of additional information about the match and a link to the Rfam database. You can achieve this by the following lines in trackDb.ra:

type bedDetail 14
url http://rfam.xfam.org/family/$$
urlLabel Rfam:

Example of BEDdetail format for a Rfam match (items should be tab-separated, the last column starts at "truncated:")

chrom chromStart chromEnd name score strand thickStart thickEnd reserved blockCount blockSizes chromStarts id description
contigA 75109 75380 Fungi_SRP-1 1002 - 75109 75109 0 1 271 0 RF01502 truncated: no, E-value: 3.5e-19

• Further things which you might want to explore:
  • Remove matches that correspond to tRNAScan-SE matches (try tool overlapSelect)
  • From several overlapping matches keep only the strongest (try tool overlapSelect)
  • More ambitious: Explore creating image of each RNA structure and somehow linking it to the info page for the match (as in non-coding RNA track in the human genome browser - see for example http://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr1%3A16520585%2D16520658, display non-coding RNA track and click on the tRNA match)

Information for users

• Each track should provide basic information for users in the HTML document displayed after clicking on track name or left bar of the browser image.
• The information should summarize what is displayed, what was source of the data, what program was used to produce the results etc
  • keep it less technical, with a link to your github wiki page for the track for potential developers replicating your work
• See examples for tracks on the http://genome-euro.ucsc.edu/ browser
• Also, the genome as a whole should have a description page. On the title page of http://genome-euro.ucsc.edu/ you see details of the selected assembly, e.g. for the guinea pig genome you see text

Guinea pig Genome Browser - cavPor3 assembly
The Feb. 2008 Cavia porcellus draft assembly (Broad Institute cavPor3) was produced by the Broad Institute at MIT and Harvard.
...

• You should create some explanatory text for you species and genome and make it display on the title page
  • This already works for Yarrowia lipolitica on genomika server, so you can try to find out how it was done

MalSym group

Clickable genes

• If you click on a gene or other displayed item in a well-setup genome browser, you get a page with more information about this item
• This does not work satisfactorily on our genomika browser
• Look at all tracks displaying gene information in four browsers:
  • sacCer3 in original UCSC genome browser [1], tracks NCBI RefSeq, SGD Genes, Ensembl Genes
  • sacCer3 in our genomika genome browser [2], tracks
  • yarLip1 in our genomika genome browser [3], tracks Ens. Genes (L), RefSeq Genes (L)
  • malSym1 in our genomika genome browser [4], track
• For each explored track find out what gets displayed after clicking at a gene, whether there are any error messages, whether the page contains a link to the source database (e.g. Ensembl, RefSeq, NCBI, SGD)

Information for users

• Each track should provide basic information for users in the HTML document displayed after clicking on track name or left bar of the browser image.
• The information should summarize what is displayed, what was source of the data, what program was used to produce the results etc
  • keep it less technical, with a link to your github wiki page for the track for potential developers replicating your work
• See examples for tracks on the http://genome-euro.ucsc.edu/ browser
• Also, the genome as a whole should have a description page. On the title page of http://genome-euro.ucsc.edu/ you see details of the selected assembly, e.g. for the guinea pig genome you see text

Guinea pig Genome Browser - cavPor3 assembly
The Feb. 2008 Cavia porcellus draft assembly (Broad Institute cavPor3) was produced by the Broad Institute at MIT and Harvard.
...

• You should create some explanatory text for you species and genome and make it display on the title page
  • This already works for Yarrowia lipolitica on genomika server, so you can try to find out how it was done