[FEAT] Genomic contexts

[jananiravi]

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

• NCBI Genome ProtMap
• 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

Predicting operons

• Operon-mapper | 2018, Bioinformatics, Merino Lab

• MicrobesOnline Operon predictions | 2005, NAR, Price, ... Arkin

• OperonHunter, using visual representation learning | 2021, Sci Reports, Assaf, ... Stevens (Rick Stevens, BV-BRC PI)

• @epbrenner: please add other papers from your list too

[jananiravi]

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

[daud99]

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

[jananiravi]

That's excellent, @daud99! Welcome aboard! Are you an outreachy applicant, too? If so, please email me & I can add you to Slack.

I converted this to discussions before noticing your comment -- so, I cannot assign you. But please keep the discussion going & get started on your PR. How do you plan to broach this? @epbrenner will be your primary contact (starting next week).

[daud99]

done @jananiravi

[jananiravi]

@epbrenner, edited the original note and added an operon prediction section above, too. Hopefully, in addition to laying out genomic neighborhood, this provides additional context.