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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Seedability: optimizing alignment parameters for sensitive sequence comparison.

Lorraine A K Ayad¹, Rayan Chikhi², Solon P Pissis^3,4

¹Department of Computer Science, Brunel University London, London UB8 3PH, UK.

Bioinformatics Advances

|August 25, 2023

Summary

This summary is machine-generated.

This study introduces Seedability, a framework to find optimal k-mer lengths for faster and more sensitive sequence alignments, especially for short and divergent DNA sequences.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Sequence alignment is crucial in bioinformatics.
Current tools often use fixed k-mer lengths, potentially limiting sensitivity.
Optimizing k-mer length is vital for accurate alignment, especially for short sequences.

Purpose of the Study:

To develop a framework for estimating optimal seed k-mer length and minimum shared seeds.
To improve the sensitivity of pairwise alignment for short and divergent sequences.
To provide a method for selecting appropriate parameters in seed-based alignment tools.

Main Methods:

Developed Seedability, a seed-based alignment framework.
Implemented a method to estimate optimal k-mer length based on alignment identity.
Evaluated performance using short and divergent sequence alignments.

Main Results:

Seedability determined parameter values that improved alignments of short and divergent sequences compared to default values.
Demonstrated cases where default parameters failed to produce alignments, but Seedability-derived parameters yielded plausible results.
Showcased enhanced sensitivity in pairwise alignment of challenging sequence pairs.

Conclusions:

The Seedability framework effectively identifies optimal k-mer lengths for enhanced sequence alignment sensitivity.
Parameter optimization using Seedability leads to more robust and accurate alignments, particularly for difficult sequence types.
This approach offers a valuable tool for improving the performance of existing bioinformatics alignment software.