Overview

This is a species-agnostic, algorithm extensible, sequence-anonymous (genome, metagenomes) gene finder library for the Julia Language.

The main goal is to create a versatile module that enables apply different implemented algorithm to DNA sequences. See, for instance, BioAlignment implementations of different sequence alignment algorithms (local, global, edit-distance).

Installation

You can install GeneFinder from the julia REPL. Press ] to enter pkg mode, and enter the following:

add GeneFinder

If you are interested in the cutting edge of the development, please check out the master branch to try new features before release.

Algorithms

Coding genes (CDS - ORFs)

  • ☒ Simple finder
  • ☐ EasyGene
  • ☐ GLIMMER
  • ☐ Prodigal - Pyrodigal
  • ☐ PHANOTATE
  • ☐ k-mer based gene finders (?)
  • ☐ Augustus (?)

Non-coding genes (RNA)

  • ☐ Infernal
  • ☐ tRNAscan

Other features

  • ☐ parallelism SIMD ?
  • ☐ memory management (?)
  • ☐ incorporate Ribosime Binding Sites (RBS)
  • ☐ incorporate Programmed Reading Frame Shifting (PRFS)
  • ☐ specialized types
    • ☒ Gene
    • ☒ ORF
    • ☒ Codon
    • ☒ CDS
    • ☐ EukaryoticGene (?)
    • ☐ ProkaryoticGene (?)
    • ☐ Intron
    • ☐ Exon
    • ☐ GFF –\> See other packages
    • ☐ FASTX –\> See I/O in other packages

Compatibilities

Must interact with or extend:

  • GenomicAnnotations.jl
  • BioSequences.jl
  • SequenceVariation.jl
  • GenomicFeatures.jl
  • FASTX.jl
  • Kmers.jl
  • Graphs.jl

Contributing

Citing

See CITATION.bib for the relevant reference(s).