deFUME

deFUME processes Sanger sequencing reads from functional metagenomic selections to assemble sequences, predict open reading frames, and annotate and visualize gene functions using BLAST, InterPro, and Gene Ontology (GO) classifiers.

Key Features:

• Integrated Workflow: Consolidates read assembly, ORF prediction, annotation, and visualization into a single automated workflow.
• Read Assembly: Assembles Sanger sequencing reads into contiguous sequences.
• Open Reading Frame (ORF) Prediction: Identifies potential ORFs within assembled sequences.
• Annotation: Annotates predicted ORFs using BLAST for sequence similarity, InterPro for domain identification, and Gene Ontology (GO) classifiers for functional terms.
• Dynamic Visualization: Generates dynamic visual representations of annotated sequences and distribution patterns.
• Comprehensive Data Overview: Produces summarized visual overviews linking raw sequence data to annotated functional outputs.

Scientific Applications:

• Functional metagenomics: Identification and characterization of novel genes recovered from functional selections of complex environmental samples.
• Microbial diversity and ecology: Analysis of annotated gene functions to support studies of microbial diversity and ecological function.

Methodology:

Users provide raw Sanger sequencing reads; the pipeline assembles reads, predicts ORFs, annotates using BLAST, InterPro, and Gene Ontology classifiers, and generates visualizations of the annotated data.