Common bioinformatics database construction

sy520

Last update: Jan 4, 2022

Related tags

Data Analysis biodb

Overview

biodb

Common bioinformatics database construction

1.taxonomy （Substance classification database）

Download the database

wget -c https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
tar -zxvf new_taxdump.tar.gz
lineage2tax.py fullnamelineage.dmp >species.taxonomy
get_taxid.py rankedlineage.dmp --kingdom Bacteria >Bacteria.taxid

2.Rfam

Download the database

family.txt gunzip Rfam.cm.gz cmpress Rfam.cm ">

wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/Rfam.cm.gz
wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/rfam2go/rfam2go
wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/database_files/family.txt.gz
zcat family.txt.gz |awk -F '\t' '{print $1"\t"$2"\t"$4"\t"$19"\t"$30}' >family.txt
gunzip Rfam.cm.gz
cmpress Rfam.cm

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