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
  • More ambititios: 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 - go to http://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr1%3A16520585%2D16520658 &hgsid=227581906_XP4IhUVhkFQJxrfo1G3SjDkZZFkI chr1:16520585-16520658

http://genome-euro.ucsc.edu/cgi-bin/hgc?c=chr1&l=16512339&r=16554600&o=16520584&t=16520658&g=tRNAs&i=tRNA%2DAsn%2DGTT%2Dchr1%2D140

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, but