Pokusime se anotovat chr21 genomu cloveka na vyskyt 5' a 3' regulacnich sekvenci genu a trasnpozonu.

1) ziskejte sekvenci chr21 cloveka (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/) a v prostredi R/Bioconductor knihovna https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html

2) Identifikujte v sekvenci DNA a ulozte do anotacniho formatu BED/GFF3:

Table Browser

- promotory (pozice -2000 <=> -1 vuci TSS)

- geny (od pocatku do konce transkripce)

BLAT

- rDNA (sekvence ribozomalni DNA dohledejte pres NCBI, treba 5S rDNA, pripadne 45S rDNA, viz https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073466/ https://www.ebi.ac.uk/ena/browser/view/X71801)

R/Bioconductor nebo jinak (Biopython, Biopieces, Biojava, vlastni kod)

https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html

https://bioconductor.org/packages/release/bioc/html/Biostrings.html matchPatterns()

https://genomicsclass.github.io/book/pages/iranges_granges.html

rtracklayer - export.gff3()

- TATATAA

- AATAAA

- konzervovanou cast reverzni transkriptazy https://prosite.expasy.org/PS50878, viz logo

3) Vytvorte Custom Track pro Genome Browser (6bodu)

4) Vytvorte vlastni Track Hub pro Genome Browser s barevnym rozlisenim regulacnich motivu (6 bodu)