GeneFinder.jl

A Gene Finder framework for Julia.
Author camilogarciabotero
Website Github
Popularity
7 Stars
Updated Last
1 Year Ago
Started In
December 2022


A Gene Finder framework for Julia.

DOI

Overview

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

The main goal of GeneFinder 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.

Example

The first implemented function is findorfs a very non-restrictive ORF finder function that will catch all ORFs in a dedicated structure. Note that this will catch random ORFs not necesarily genes since it has no ORFs size or overlapping condition contraints. Thus it might consider aa"M*" a posible encoding protein from the resulting ORFs.

using BioSequences, GeneFinder

# > 180195.SAMN03785337.LFLS01000089 -> finds only 1 gene in Prodigal (from Pyrodigal tests)
seq = dna"AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAACAGCACTGGCAATCTGACTGTGGGCGGTGTTACCAACGGCACTGCTACTACTGGCAACATCGCACTGACCGGTAACAATGCGCTGAGCGGTCCGGTCAATCTGAATGCGTCGAATGGCACGGTGACCTTGAACACGACCGGCAATACCACGCTCGGTAACGTGACGGCACAAGGCAATGTGACGACCAATGTGTCCAACGGCAGTCTGACGGTTACCGGCAATACGACAGGTGCCAACACCAACCTCAGTGCCAGCGGCAACCTGACCGTGGGTAACCAGGGCAATATCAGTACCGCAGGCAATGCAACCCTGACGGCCGGCGACAACCTGACGAGCACTGGCAATCTGACTGTGGGCGGCGTCACCAACGGCACGGCCACCACCGGCAACATCGCGCTGACCGGTAACAATGCACTGGCTGGTCCTGTCAATCTGAACGCGCCGAACGGCACCGTGACCCTGAACACAACCGGCAATACCACGCTGGGTAATGTCACCGCACAAGGCAATGTGACGACTAATGTGTCCAACGGCAGCCTGACAGTCGCTGGCAATACCACAGGTGCCAACACCAACCTGAGTGCCAGCGGCAATCTGACCGTGGGCAACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAGC"

Finding all ORFs, the CDS and Proteins

findorfs(seq)

12-element Vector{ORF}:
 ORF(29:40, '+')
 ORF(137:145, '+')
 ORF(164:184, '+')
 ORF(173:184, '+')
 ORF(236:241, '+')
 ORF(248:268, '+')
 ORF(362:373, '+')
 ORF(470:496, '+')
 ORF(551:574, '+')
 ORF(569:574, '+')
 ORF(581:601, '+')
 ORF(695:706, '+')

Two other functions (get_cds and get_proteins) pass the sequence to findorfs take the ORFs and act as generators of the sequence, so this way the can be collected in the REPL as an standard output or writteen into a file more conviniently using the FASTX IO system:

get_cds(seq)

12-element Vector{LongSequence{DNAAlphabet{4}}}:
 ATGCAACCCTGA
 ATGCGCTGA
 ATGCGTCGAATGGCACGGTGA
 ATGGCACGGTGA
 ATGTGA
 ATGTGTCCAACGGCAGTCTGA
 ATGCAACCCTGA
 ATGCACTGGCTGGTCCTGTCAATCTGA
 ATGTCACCGCACAAGGCAATGTGA
 ATGTGA
 ATGTGTCCAACGGCAGCCTGA
 ATGCAACCCTGA
get_proteins(seq)

12-element Vector{LongAA}:
 MQP*
 MR*
 MRRMAR*
 MAR*
 M*
 MCPTAV*
 MQP*
 MHWLVLSI*
 MSPHKAM*
 M*
 MCPTAA*
 MQP*

Writting cds, proteins fastas and bed file

write_cds("cds.fasta", seq)
cat cds.fasta

>location=29:40 strand=+
ATGCAACCCTGA
>location=137:145 strand=+
ATGCGCTGA
>location=164:184 strand=+
ATGCGTCGAATGGCACGGTGA
>location=173:184 strand=+
ATGGCACGGTGA
>location=236:241 strand=+
ATGTGA
>location=248:268 strand=+
ATGTGTCCAACGGCAGTCTGA
>location=362:373 strand=+
ATGCAACCCTGA
>location=470:496 strand=+
ATGCACTGGCTGGTCCTGTCAATCTGA
>location=551:574 strand=+
ATGTCACCGCACAAGGCAATGTGA
>location=569:574 strand=+
ATGTGA
>location=581:601 strand=+
ATGTGTCCAACGGCAGCCTGA
>location=695:706 strand=+
ATGCAACCCTGA
write_proteins("proteins.fasta", seq)
cat proteins.fasta

>location=29:40 strand=+
MQP*
>location=137:145 strand=+
MR*
>location=164:184 strand=+
MRRMAR*
>location=173:184 strand=+
MAR*
>location=236:241 strand=+
M*
>location=248:268 strand=+
MCPTAV*
>location=362:373 strand=+
MQP*
>location=470:496 strand=+
MHWLVLSI*
>location=551:574 strand=+
MSPHKAM*
>location=569:574 strand=+
M*
>location=581:601 strand=+
MCPTAA*
>location=695:706 strand=+
MQP*
write_bed("cds.bed", seq)
cat cds.bed

29	40	+
137	145	+
164	184	+
173	184	+
236	241	+
248	268	+
362	373	+
470	496	+
551	574	+
569	574	+
581	601	+
695	706	+

Combining FASTX for reading and writing fastas

using FASTX

write_proteins("test/data/NC_001884.fasta", "proteins.fasta")
head proteins.fasta

>location=75:113 strand=+
MKLNLRIGVISN*
>location=144:215 strand=+
MLTITSFKTILNSSFFFSELDSM*
>location=210:215 strand=+
M*
>location=237:374 strand=+
MLFLTVLLSISDCVSCNPLSSFFAFWSSLNSSSNAAFLFKKSSSL*
>location=337:402 strand=+
MQLFSSKKVHHCKCHFHIYRR*

Algorithms

Coding genes (CDS - ORFs)

  • Simple finder
  • EasyGene
  • GLIMER3
  • Prodigal - Pyrodigal
  • PHANOTATE
  • k-mer based gene finders (?)
  • Augustus (?)

Non-coding genes (RNA)

  • Infernal
  • tRNAscan

Contributing

Citing

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

Required Packages

Used By Packages

No packages found.