TriFLe

TriFLe simulates terminal restriction fragments (T-RFs) from user-supplied DNA sequences to generate theoretical T-RF profiles for species identification and interpretation of T-RFLP (Terminal Restriction Fragment Length Polymorphism) data.

Key Features:

• Theoretical T-RF Generation: Generates theoretical T-RFs from user-defined sequences, including sequences derived from clone libraries and specific genes.
• Polymorphic Enzyme Identification: Identifies the most polymorphic restriction enzymes suitable for producing distinct T-RF patterns from the input sequence set.
• T-RF Collection Creation: Compiles collections of predicted T-RFs corresponding to the provided dataset for downstream analysis and comparison.
• Comparison with Experimental Data: Matches theoretical T-RFs against experimental T-RFLP patterns to identify specific T-RFs within empirical datasets.

Scientific Applications:

• Microbial community profiling: Analyzing complex microbial communities in microbial ecology and environmental microbiology using T-RFLP data.
• Gene-specific T-RFLP analysis: Studying amoA and pmoA genes to investigate nitrogen and methane cycles through T-RF profiling.
• Environmental stratification studies: Identifying overlapping populations of ammonia-oxidizing bacteria (AOB) and methane-oxidizing bacteria (MOB) within strata such as the metalimnion of subtropical lakes.

Methodology:

Simulating T-RFs from user-provided sequences using selected restriction enzymes, predicting polymorphic restriction enzyme sites, generating theoretical T-RF profiles, and comparing theoretical T-RFs to experimental T-RFLP patterns.