smallgenes

Small eukaryotic genes in small genomic contexts.

Background

Genes and genomes can vary in size from small to HUGE. Smaller genes are useful for development, testing, and tutorials. This project seeks to create a set of small genes for a variety of common genomes.

A smallgene locus has the following features:

• The DNA is represented in a FASTA file
• The annotation is represented in a GFF3 file
• There is 1 protein-coding gene whose length is short (e.g < 1000 bp)
• The gene is flanked by a little genomic sequence (e.g. 99 bp)
• The gene is moderately to highly expressed
• All introns follow the GT-AG rule
• Intron and exon lengths are not unusually short or long
• The gene is not too similar to other genes in the set

Genomes

Initial smallgene sets are built for the following genomes.

• A. thaliana
• C. elegans
• D. melanogaster

Build Procedure

The build procedure for each genome requires some customization due to differences in the way each community represents its GFF.

Some software is required:

• git clone KorfLab/grimoire
  • add grimoire/grimoire to your PYTHONPATH
  • add grimoire/haman to your PATH
• git clone KorfLab/isoforms -add isoforms to your PYTHONPATH
• install blastn (e.g. via mini-conda)

C. elegans

Note: this is copied over from datacore2024 and has not been validated yet

In the lines below, $DATA is wherever you keep your data.

mkdir build
cd build
ln -s $DATA/c_elegans.PRJNA13758.WS282.genomic.fa.gz genome.gz
ln -s $DATA/c_elegans.PRJNA13758.WS282.annotations.gff3.gz gff3.gz
gunzip -c gff3.gz | grep -E "WormBase|RNASeq" > ws282.gff3
cd ..
haman build/genome.gz build/ws282.gff3 pcg genes --issuesok --plus
python3 src/gene_selector.py build/genes

This results in 2 new file: initial.genes.txt and initial.log.json

Some of the genes are duplicates or near duplicates. The next step trims the set to be more unique.

perl src/gene_reducer.pl

This results in the smallgenes directory, which has 1045 genes. The final step is to rename the directory to the genome and create a tar-ball.

mv smallgenes c.elegans.smallgenes
tar -czf c.elegans.smallgenes.tar.gz c.elegans.smallgenes

D. melanogaster

A. thaliana