G-language API

G-language API provides a collection of computational methods for bacterial genome analysis, including binding-site identification using information theory, nucleotide composition and oligonucleotide distribution analysis, codon usage bias calculation, gene expression prediction, and genomic data visualization.

Key Features:

• Comprehensive program suite: Over 100 specialized programs comprising 145 functions for genomic analyses.
• Binding-site identification: Identification of binding sites using information theory principles.
• Nucleotide composition analysis: Analysis of nucleotide composition bias.
• Oligonucleotide distribution analysis: Examination of oligonucleotide distribution patterns across genomes.
• Codon usage and expression prediction: Calculation of codon usage bias and prediction of gene expression levels.
• Visualization: Capabilities for visualizing genomic data and analysis results.
• REST services: REST interface exposing 145 functions identified by URIs.
• SOAP services: SOAP-based services exposing 77 programs with a WSDL for workflow integration (e.g., Taverna).

Scientific Applications:

• Bacterial genomics: Comparative and detailed analyses of bacterial genomes.
• Regulatory sequence analysis: Discovery and characterization of transcription factor binding sites using information theory.
• Genome composition studies: Investigation of nucleotide composition bias and oligonucleotide distribution patterns.
• Codon usage and expression studies: Comparative codon usage analyses and prediction of gene expression levels.
• Workflow integration: Incorporation of analyses into automated workflows via REST and SOAP interfaces.

Methodology:

Identification of binding sites using information theory; analysis of nucleotide composition bias; examination of oligonucleotide distribution patterns; calculation of codon usage bias and prediction of gene expression levels; programmatic access via REST (145 functions identified by URIs) and SOAP (77 programs with WSDL).