A Gene Finder framework for Julia.

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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.

Finding complete and internal (overlapped) ORFs

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"

Now lest us find the ORFs

findorfs(seq)

12-element Vector{ORF}:
 ORF(29:40, '+', 2)
 ORF(137:145, '+', 2)
 ORF(164:184, '+', 2)
 ORF(173:184, '+', 2)
 ORF(236:241, '+', 2)
 ORF(248:268, '+', 2)
 ORF(362:373, '+', 2)
 ORF(470:496, '+', 2)
 ORF(551:574, '+', 2)
 ORF(569:574, '+', 2)
 ORF(581:601, '+', 2)
 ORF(695:706, '+', 2)

Two other functions (getorfdna and getorfaa) 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:

getorfdna(seq)

12-element Vector{LongSubSeq{DNAAlphabet{4}}}:
 ATGCAACCCTGA
 ATGCGCTGA
 ATGCGTCGAATGGCACGGTGA
 ATGGCACGGTGA
 ATGTGA
 ATGTGTCCAACGGCAGTCTGA
 ATGCAACCCTGA
 ATGCACTGGCTGGTCCTGTCAATCTGA
 ATGTCACCGCACAAGGCAATGTGA
 ATGTGA
 ATGTGTCCAACGGCAGCCTGA
 ATGCAACCCTGA

getorfaa(seq)

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

Writting cds, proteins fastas, bed and gffs whether from a LongSeq or from a external fasta file.

write_cds("cds.fasta", seq)

cat cds.fasta

>location=29:40 strand=+ frame=2
ATGCAACCCTGA
>location=137:145 strand=+ frame=2
ATGCGCTGA
>location=164:184 strand=+ frame=2
ATGCGTCGAATGGCACGGTGA
>location=173:184 strand=+ frame=2
ATGGCACGGTGA
>location=236:241 strand=+ frame=2
ATGTGA
>location=248:268 strand=+ frame=2
ATGTGTCCAACGGCAGTCTGA
>location=362:373 strand=+ frame=2
ATGCAACCCTGA
>location=470:496 strand=+ frame=2
ATGCACTGGCTGGTCCTGTCAATCTGA
>location=551:574 strand=+ frame=2
ATGTCACCGCACAAGGCAATGTGA
>location=569:574 strand=+ frame=2
ATGTGA
>location=581:601 strand=+ frame=2
ATGTGTCCAACGGCAGCCTGA
>location=695:706 strand=+ frame=2
ATGCAACCCTGA

Combining FASTX for reading and writing fastas

using FASTX

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

head proteins.fasta

>location=41:145 strand=- frame=2
MTQKRKGPIPAQFEITPILRFNFIFDLTATNSFH*
>location=41:172 strand=- frame=2
MVLKDVIVNMTQKRKGPIPAQFEITPILRFNFIFDLTATNSFH*
>location=41:454 strand=- frame=2
MSEHLSQKEKELKNKENFIFDKYESGIYSDELFLKRKAALDEEFKELQNAKNELNGLQDTQSEIDSNTVRNNINKIIDQYHIESSSEKKNELLRMVLKDVIVNMTQKRKGPIPAQFEITPILRFNFIFDLTATNSFH*
>location=41:472 strand=- frame=2
MKTKKQMSEHLSQKEKELKNKENFIFDKYESGIYSDELFLKRKAALDEEFKELQNAKNELNGLQDTQSEIDSNTVRNNINKIIDQYHIESSSEKKNELLRMVLKDVIVNMTQKRKGPIPAQFEITPILRFNFIFDLTATNSFH*
>location=41:505 strand=- frame=2
MLSKYEDDNSNMKTKKQMSEHLSQKEKELKNKENFIFDKYESGIYSDELFLKRKAALDEEFKELQNAKNELNGLQDTQSEIDSNTVRNNINKIIDQYHIESSSEKKNELLRMVLKDVIVNMTQKRKGPIPAQFEITPILRFNFIFDLTATNSFH*