{"entity": "publication", "iuid": "bb8c67f4819042d8b315356452b6463c", "timestamp": "2026-08-25T23:32:00.997Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bb8c67f4819042d8b315356452b6463c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bb8c67f4819042d8b315356452b6463c"}}, "title": "InParanoiDB 9: Ortholog Groups for Protein Domains and Full-Length Proteins.", "authors": [{"family": "Persson", "given": "Emma", "initials": "E"}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}], "type": "journal article", "published": "2023-07-15", "journal": {"title": "J. Mol. Biol.", "issn": "1089-8638", "volume": "435", "issue": "14", "pages": "168001", "issn-l": "0022-2836"}, "abstract": "Prediction of orthologs is an important bioinformatics pursuit that is frequently used for inferring protein function and evolutionary analyses. The InParanoid database is a well known resource of ortholog predictions between a wide variety of organisms. Although orthologs have historically been inferred at the level of full-length protein sequences, many proteins consist of several independent protein domains that may be orthologous to domains in other proteins in a way that differs from the full-length protein case. To be able to capture all types of orthologous relations, conventional full-length protein orthologs can be complemented with orthologs inferred at the domain level. We here present InParanoiDB 9, covering 640 species and providing orthologs for both protein domains and full-length proteins. InParanoiDB 9 was built using the faster InParanoid-DIAMOND algorithm for orthology analysis, as well as Domainoid and Pfam to infer orthologous domains. InParanoiDB 9 is based on proteomes from 447 eukaryotes, 158 bacteria and 35 archaea, and includes over one billion predicted ortholog groups. A new website has been built for the database, providing multiple search options as well as visualization of groups of orthologs and orthologous domains. This release constitutes a major upgrade of the InParanoid database in terms of the number of species as well as the new capability to operate on the domain level. InParanoiDB 9 is available at https://inparanoidb.sbc.su.se/.", "doi": "10.1016/j.jmb.2023.168001", "pmid": "36764355", "labels": [], "xrefs": [{"db": "pii", "key": "S0022-2836(23)00057-8"}], "notes": [], "created": "2026-08-20T07:59:48.132Z", "modified": "2026-08-20T07:59:48.175Z"}