jananiravi commented 3 years ago

Genomic context aka neighborhood analyses

[ ] edirect and eutils to fetch genes of interest (from a list)
- [ ] + slurm
[ ] user-input: no. of neighbors on each side (default: ±7)
[ ] user-input: filter by intergenic distance (200bp)
[ ] identify orientation of genes
[ ] back to tab-delim format with <- || -> | A -> B -> C||<- D
[ ] option: indicate query with * or some other marker
[ ] first: append final GC column to the BLAST output file
[ ] add DA for each of the neighbors' accessions
[ ] finally: replace with GC column above with DA+GC A+B -> C+D

Existing tools/papers

[ ] rentrez: CRAN tutorial
[ ] Is there a way to retain intergenic distance | to use later as edge weight in networks | Check 2020 PLoSCompBio pipeline paper
[ ] MiST DB | 2020 paper mentions this | 2024 version doesn't!
[ ] COGNAT: a web server for comparative analysis of genomic neighborhoods | Klimchuk et al., Biol. Direct 2020
[ ] Systematic prediction of functionally linked genes in bacterial and archaeal genomes | Shmakov et al., Nat Protocols 2020
[ ] Gene Graphics | Harrison et al., Bioinformatics 2018
[ ] Conserved Genomic Neighborhood ... | Esch et al., BMC Bioinformatics 2020
[ ] gggenomes: https://thackl.github.io/gggenomes
[ ] GeCoViz: https://gecoviz.cgmlab.org | paper
[ ] @epbrenner: please add other papers from your list too

jananiravi commented 3 months ago

@epbrenner, here's your new companion e-book on eutils, entrez, and more! (Related: rentrez)

daud99 commented 1 month ago

@jananiravi Can you assigned this task to me. I'm an Outreachy applicant selected for this session?