REPK

REPK identifies sets of four restriction endonucleases that maximize resolution among user-specified sequence groups for terminal restriction fragment length polymorphism (T-RFLP) analysis.

Key Features:

• Restriction enzyme selection: Identifies sets of four restriction endonucleases that collectively provide optimal resolution to distinguish sequence groups.
• T-RFLP optimization: Enhances specificity and efficacy of terminal restriction fragment length polymorphism analysis through rational enzyme choice.
• Input sequence flexibility: Accepts arbitrary genetic sequences and is not limited to 16S rRNA genes.
• Taxonomic rank specification: Supports analysis and grouping at user-specified taxonomic ranks.
• Filtering options: Applies filters to refine enzyme selection based on user-defined criteria relevant to the study.

Scientific Applications:

• T-RFLP profiling: Improves resolution and specificity of microbial community fingerprinting using T-RFLP.
• Sequence-group differentiation: Facilitates unique differentiation of user-specified sequence groups across taxonomic ranks.

Methodology:

Identifies sets of four restriction endonucleases that together maximize differentiation among provided sequences and applies user-selectable filtering criteria to refine enzyme selection; accepts arbitrary genetic sequences and taxonomic-rank grouping as input.