Update in progress: note to all users. FAIRsharing is always available for you to search and discover databases, standards and data policies. However, for producers of these resources who maintain or wish to add new records, please note that editing is disabled until September while we migrate our data to our new, improved system. Read our blog post or get in touch with us for more details.
21/09/21 Ongoing Network Maintenance: From the 21st of September FAIRsharing may be offline at various point during the day; we apologise for any inconvenience.

ready PGDBj Ortholog Database

General Information
The PGDBj Ortholog Database, created under the auspices of the Plant Genome Database Japan (PGDBj), contains information about orthologous genes in plants based on their corresponding amino acid sequence similarity. By placing PGDBj Ortholog Database as a 'hub' within a suite of resources and databases, the aim is to make reciprocal links between databases containing information about various organisms. Users can find orthologs in different subsets of organisms by searching the database using either amino acid information or keywords. The PGDBj 'amino acid sequence DB' contains 500,000 amino acid sequences from 20 plant species classified in Viridiplantae. The PGDBj Ortholog Database provides gene cluster information based on amino acid sequence similarity. Over 500,000 amino acid sequences of 20 Viridiplantae species were subjected to reciprocal BLAST searches and clustered. Sequences from plant genome DBs (e.g. TAIR10 and RAP-DB) were also included in the cluster with a direct link to the original DB. To provide outgroups in the Viridiplantae comparative analyses, ortholog data sets derived from Cyanobacteria and Deuterostomia are also being analyzed.




Awaiting DOI assignment.


Record added: May 10, 2018, 2:28 p.m.
Record updated: Jan. 13, 2020, 7:21 p.m. by The FAIRsharing Team.

Show edit history


Support

General

Additional Information


Tools

    No tools defined


Access / Retrieve Data

Conditions of Use


Data Access




Publications

Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases.

Asamizu E,Ichihara H,Nakaya A,Nakamura Y,Hirakawa H,Ishii T,Tamura T,Fukami-Kobayashi K,Nakajima Y,Tabata S
Plant Cell Physiol 2013

View Paper (PubMed) View Publication

Plant Genome DataBase Japan (PGDBj).

Nakaya A,Ichihara H,Asamizu E,Shirasawa S,Nakamura Y,Tabata S,Hirakawa H
Methods Mol Biol 2016

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined


Related Databases

No related databases defined


Implementing Policies

This record is not implemented by any policy.


Credit

Record Maintainer

  • This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

Maintains