Warning this is a work in progress.

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

The main idea is to create versatile module that enables apply different implemented algorithm to DNA sequences. See the BioAlignment implementation of different sequence alignment algorithms (local, global, edit-distance).

You can install BioSequences 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.

• Simple finder (a simple ORF finder)
• Prodigal - Pyrodigal
• k-mer based (?)
• Augustus (?)
• PHANOTATE

• Infernal
• tRNAscan

• parallelism SIMD ?
• memory management (?)
• specialized types
  • Gene
  • ORF
  • CDS
  • EukaryoticGene (?)
  • ProkaryoticGene (?)
  • Codon
  • Intron
  • Exon
  • GFF --> See other packages
  • FASTX --> See I/O in other packages

Must interact with or extend:

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

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