Download InParanoiDB 9 sources

Download Species List

A list of all InParanoiDB 9 species can be downloaded here. The list contains the following columns:

NCBITaxID,UniProtID,Species_name,Domain

Download Species List

Download Proteomes

All InParanoiDB9 proteomes are originally fetched from UniProt. Here you can download the proteomes for all species, where the fasta headers have been filtered to only contain the protein name.

Find your species

Download Proteome

Download Domain-split Proteomes

Here you can download proteomes files where the proteins are split up into their corresponding pfam domains, used for running Domainoid. The fasta headers in the file correspond to:

Protein name || Protein length _ Domain start coordinate _ Domain stop coordiate _ Domain length

Find your species

Download domain-split Proteome

Download Pairwise ortholog files

Here you can download all orthologs for a pair of species, generated from InParanoid. The files can be downloaded in SQLtabe-format, or OrthoXML format. The SQLtable format includes a tab-separated text file containing the groups of orthologs generated for your species. It lists each protein in a separate row, hence having multiple rows for each ortholog group. The SQLtable-file contains the following columns:

Group-id Bitscore Species Inparalog-score Protein-name Seed-score

Find your first species

Find your second species

SQLtable orthoXml Select type of file to download

Download Pairwise orthologs

Download Pairwise Domain-ortholog files

Here you can download all domain orthologs for a pair of species, generated from Domainoid. The files can be downloaded in SQLtabe-format, or OrthoXML format. The SQLtable format includes a tab-separated text file containing the groups of orthologs generated for your species. It lists each protein in a separate row, hence having multiple rows for each ortholog group. The SQLtable-file contains the following columns:

Group-id Bitscore Species Inparalog-score Protein-name||SequenceLength_DomainLength_DomainStartCoordinate_DomainStopCoordinate_DomainId Seed-score

Find your first species

Find your second species

SQLtable orthoXml Select type of file to download

Download Pairwise orthologs

Download over API

You can also download the data using the inParanoiDB9 APIs

Download a proteome

inparanoidb.sbc.su.se/download/proteome/taxID&prot

Download a Domain-split proteome

inparanoidb.sbc.su.se/download/proteome/taxID&dom

Download a pairwise ortholog file

inparanoidb.sbc.su.se/download/sqltable/taxIdA&taxIdB&prot

Download a pairwise domain-ortholog file

inparanoidb.sbc.su.se/download/sqltable/taxIdA&taxIdB&dom

Download Previous versions of InParanoiDB

Choose a version and a file type below to download data from previous InParanoiDB versions

v.8.0 v.7.0 v.6.1 v.6.0 v.5.1 v.5.0 v.4.0 v.3.0 v.2.0 Select InParanoiDB version to download

SQLtable-files Sequences Select type of file to download

Download

All previous versions are available in SQLtable format. If you want to use the orthologs in orthoXML format, you can convert them, using the script provided here.

python3 sqltableToOrthoxml.py -i /directory/of/your/SQLtable/files

Download OrthoXml conversion script

Download InParanoidUniProtXref

Download a list of all UniProt protein identifiers used in InParanoiDB

Download InParanoidUniProtXref.txt