Fishes

Finding pseudogenes in fish genomes

Disclaimer: use at your own risk. No guarantees whatsoever. We present these to try and ensure reproducibility of our work.

Downloading genomes:

To download the fish genomes we worked with, we used NCBI's "datasets" and "dataformat" commands from: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/download-and-install/

These can be installed, in a mac, suing the 'installNCBIcli.zsh' script found in the https://github.com/Computational-conSequences/NCBIGenomes repository.

The commands used, also from the https://github.com/Computational-conSequences/NCBIGenomes repository:

zsh ~/Programitas/GENOMEDB/DownLoad/DownLoadNCBI/bringMetadata.zsh Actinopterygii
zsh ~/Programitas/GENOMEDB/DownLoad/DownLoadNCBI/bringGenomes.zsh Actinopterygii

The order is important, the first command downloads the information about these genomes, producing a list of identifiers to then be used to download the genomes, and organize the files in such genomes, under specific directories that make it easier for our downstream analyses to proceed.

Downloading sequences of proteins of interest for the project:

xxxx

formating blast genome databases:

To format the databases, we have produced a buildBlastDB.zsh script, which should be run after downloading the genomes, since it expects the dorectories fna-Actinopterygii and faa-Actinopterygii to be there, and contains these loops:

mkdir -p blastnDB
echo "building blastn genome databases"
for FILE in fna-Actinopterygii/GC*.fna.gz
do
    makeblastdb \
        -in $FILE \
        -dbtype nucl \
        -out blastnDB/$FILE:t:r:r \
        -title $FILE:t:r:r \
        -parse_seqids
done
#echo "done building databases"

mkdir -p blastpDB
echo "building blastp genome databases"
for FILE in faa-Actinopterygii/GC*.faa.gz
do
    makeblastdb \
        -in $FILE \
        -dbtype prot \
        -out blastpDB/$FILE:t:r:r \
        -title $FILE:t:r:r \
        -parse_seqids
done
echo "done building databases"