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).