DCMF

DCMF performs genome sequencing simulation and analysis, integrating PacBio whole-genome SMRT sequencing, Illumina error correction, IMG pipeline annotation, phylogenetic analysis, and metabolic gene profiling.

Key Features:

• Whole Genome Sequencing: De novo, gap-free assembly of the DCMF genome from PacBio SMRT sequencing reads.
• Error Correction: Illumina reads used to correct minor insertions and deletions (indels) in the assembly.
• Genomic Annotation: Predicted 5,773 protein-coding genes annotated using the IMG pipeline.
• Phylogenetic Analysis: Classification based on 16S rRNA gene sequences and predicted proteome data identifying DCMF as a novel Peptococcaceae member.
• Metabolic Insights: Identification of 96 methylamine methyltransferases suggesting roles in dichloromethane (DCM) degradation.
• Bioinformatics Resources: Custom genome browser and search tool providing multiple sequence alignments and phylogenetic trees for every predicted protein.

Scientific Applications:

• Microbial Bioremediation: Supports studies on DCMF's ability to degrade dichloromethane, informing development of bioremediation strategies.

Methodology:

De novo gap-free assembly from PacBio SMRT reads; Illumina-based correction of indels; gene prediction and annotation via the IMG pipeline (5,773 predicted genes); phylogenetic analysis using 16S rRNA gene sequences and predicted proteome; generation of multiple sequence alignments and phylogenetic trees for each predicted protein.