Abstract
Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use.
Highlights
The advent and continued rise of Generation DNA sequencing has enabled microbiologists to investigate more and more microbes on a genome level
GAMOLA2 utilizes recognized tools with known performance parameters that are combined into a single source of information
of the primary objectives in the subsequent data analyses is the identification of genes
Summary
The advent and continued rise of Generation DNA sequencing has enabled microbiologists to investigate more and more microbes on a genome level. In 2003 the prokaryotic genome annotation pipeline GAMOLA (Altermann and Klaenhammer, 2003) was developed with the aim of providing microbiologists with a user friendly system for effective and reliable (draft) genome annotation. A number of other genome annotation systems have been established—ranging widely in scope, functionality and data analysis philosophies. While GAMOLA2 requires a Linux based system to generate the comprehensive genome annotation, the use of a customized version of the Artemis Java application (Rutherford et al, 2000) ensures platform independence for subsequent expert curation and analyses. The GAMOLA2/Artemis software package is available free of charge for academic use
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