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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program.

Michel Schneider¹, Lydie Lane, Emmanuel Boutet

¹Swiss Institute of Bioinformatics, Centre Médical Universitaire, Genève 4, Switzerland. Michel.Schneider@isb-sib.ch

Journal of Proteomics

|December 17, 2008

Summary

This summary is machine-generated.

The UniProt knowledgebase (UniProtKB) offers comprehensive protein data, including manually curated plant proteome information for model organisms like Arabidopsis thaliana and Oryza sativa.

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Area of Science:

Bioinformatics
Proteomics
Plant Biology

Background:

The UniProt knowledgebase (UniProtKB) is a central resource for protein sequence and functional information.
UniProtKB comprises manually curated (Swiss-Prot) and automatically annotated (TrEMBL) sections, covering proteins from public nucleotide sequence databases.
The Plant Proteome Annotation Program (PPAP) specifically targets manual annotation of plant proteins.

Purpose of the Study:

To detail the structure and content of the UniProt knowledgebase (UniProtKB).
To highlight the role of the Plant Proteome Annotation Program (PPAP) in annotating plant-specific proteins.
To describe the manual curation process and data integration within UniProtKB/Swiss-Prot, focusing on model plants.

Main Methods:

Manual curation of protein sequences and functional data.
Integration of data from diverse sources, including ESTs, transcripts, and homologous proteins.
Annotation of post-translational modifications (PTM) and mass spectrometry (MS) experimental results.

Main Results:

UniProtKB/Swiss-Prot provides a non-redundant, manually curated collection of plant protein information.
Focus on Arabidopsis thaliana and Oryza sativa proteomes, with detailed annotation of isoforms.
Inclusion of experimental proteomics data enhances the value of curated entries.

Conclusions:

UniProtKB is a vital resource for plant science research, offering high-quality annotated proteome data.
Manual curation ensures data accuracy and facilitates the reconstruction of protein isoforms and functional information.
The PPAP contributes significantly to understanding plant proteomes, particularly for model organisms.