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GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
John Besemer1, Mark Borodovsky
1School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Nucleic Acids Research
|June 28, 2005
Summary
GeneMark web software offers reliable gene identification for prokaryotic, eukaryotic, and viral genomes. It provides species-specific models and the GeneMarkS tool for novel sequences, aiding genomic research.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Gene identification is crucial for understanding genome function.
- Researchers face challenges in accurately identifying genes in diverse genomic sequences.
Purpose of the Study:
- To introduce the GeneMark web software as a solution for gene identification.
- To highlight the capabilities of GeneMark for various genome types and novel sequences.
Main Methods:
- Utilizing the GeneMark family of programs for gene prediction.
- Employing species-specific pre-computed gene models for known genomes.
- Applying GeneMarkS for *de novo* gene identification in novel prokaryotic sequences.
Main Results:
- The GeneMark server facilitates gene prediction across prokaryotic, eukaryotic, and viral genomes.
- It offers analysis for ~200 prokaryotic and >10 eukaryotic genomes with pre-computed models.
- GeneMarkS provides *de novo* gene identification and a database of over 1000 reannotated viral genomes.
Conclusions:
- GeneMark web software provides a convenient and reliable platform for gene identification.
- The software supports diverse genomic analyses, including novel sequence annotation.
- Regular updates ensure access to the latest gene prediction tools and models.