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ben-silke / biol3209

This repo contains the code for the undertaking of the biol3209 subject.
BSD 3-Clause "New" or "Revised" License
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Literature review - what are the current methods for gene identification? #5

Open ben-silke opened 2 years ago

ben-silke commented 2 years ago

Prokaryotic gene identification tools:

genemark2-s GeneMark2 is a prokaryotic gene identification tool. It is largely built upon the idea of predicting gene starts.

Prediction of protein coding ORF's.

  1. GeneMarkS,
  2. Glimmer3,
  3. Prodigal.
ben-silke commented 2 years ago

GeneMarkS-2 and GeneMarkS

These tools rely on machine learning to predict the start position accounting for the atypical start sites of prokaryotes

ben-silke commented 2 years ago

Prodigal:

ben-silke commented 2 years ago

There seems to be two classes/ problems (at minimum).

  1. finding genes.
  2. finding orthologs

I am rather confused about the difference between these two problems.

most especially; the finding genes algorithms are really complex; whereas the finding orthologs program is so basic This is not such a criticism of the code; though that should also be criticised; but the machine learning methods seem to take into a number of potentials; which are holistically ignored by JustOrthologs