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R-package for an Ultra-Fast and Comprehensive Gene Annotation in Plants
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README.md

Hayai-Annotation Plants v1.0.2

R-package for an Ultra-Fast and Comprehensive Gene Annotation in Plants

Description

Hayai-Annotation-Plants is an R-package with a shiny-browser interface for a highly accurate and fast gene annotation system for plant species (Embryophyta).

Hayai-Annotation-Plants provides five levels of annotation:

  1. Protein Name;
  2. Gene Ontology (GO) consisting of three main domains (Biological Process, Molecular Function and Cellular Component);
  3. Enzyme Commission Code - EC;
  4. Protein Existence Level;
  5. Evidence Code for GO annotation.

Documentation

For downloading, installing and running Hayai-Annotation Plants please see Hayai-Annotation-Plants wiki

Reference

Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants
Andrea Ghelfi, Kenta Shirasawa, Hideki Hirakawa, Sachiko Isobe
Bioinformatics, btz380, https://doi.org/10.1093/bioinformatics/btz380

Updates

2019/07/05. Update database on 2019/06/21.
Taxonomy Viridiplantae were implemented, now it includes algae.
Database were clustered to 99% sequence identity and a new algorithm were implemented to make Hayai-annotation Plants faster

2019/06/20. Hayai-annotation Plants v1.0.1 on Docker Container. Recommended for up to 2,000 sequences.

2019/01/04. Low number of input sequences crash - Fixed. Now, graphics are generated if number of annotated queries are higher than 500.
Hayai-Annotation Plants run with even if USEARCH is installed in another directory (requires symbolic link).

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