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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
Published on: June 8, 2020
Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
Gregory E Sims1, Se-Ran Jun, Guohong A Wu
1Department of Chemistry, University of California, Berkeley, CA 94720, USA.
Summary
Comparing whole genomes requires alignment-free methods like feature frequency profiles (FFP). This study optimizes FFP by determining the ideal l-mer range, demonstrating its effectiveness in reconstructing mammalian phylogeny from intronic sequences.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Traditional whole-genome comparison methods like multiple sequence alignment are unsuitable for distantly related genomes.
- Alignment-free approaches using feature (or l-mer) frequency profiles (FFP) offer an alternative for genomic comparisons.
- Identifying the optimal resolution range of l-mers is crucial for the accuracy of FFP-based comparisons.
Purpose of the Study:
- To introduce and validate an optimized feature frequency profile (FFP) method for whole-genome comparison.
- To determine the optimal resolution range of l-mers for accurate genomic comparisons.
- To demonstrate the utility of the optimized FFP method in phylogenetic reconstruction.
Main Methods:
- The method involves determining the optimal l-mer resolution range using text-based comparisons (English books).
- Robustness of the optimized FFP method was tested using a nucleotide-level mutation model.
- Phylogenetic trees were reconstructed using FFP from concatenated mammalian intronic sequences.
Main Results:
- The optimized FFP method effectively determines the optimal l-mer resolution range for genomic comparisons.
- The FFP method demonstrated robustness against various base substitutions and rearrangements at the nucleotide level.
- Phylogenetic trees derived from intronic sequences using FFP were consistent with established mammalian phylogeny.
Conclusions:
- The optimized feature frequency profile (FFP) method provides an effective alignment-free approach for whole-genome comparison.
- Intronic genomic regions contain a phylogenic signal comparable to coding regions, suitable for phylogenetic analysis.
- The FFP method is valuable for comparing large genomic regions, even those lacking highly homologous genes.
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