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A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

ALP & FALP: C++ libraries for pairwise local alignment E-values.

Sergey Sheetlin¹, Yonil Park¹, Martin C Frith²

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD 20894, USA and.

Bioinformatics (Oxford, England)

|October 3, 2015

Summary

This summary is machine-generated.

The Ascending Ladder Program (ALP) and Frameshift Ascending Ladder Program (FALP) provide rapid E-value calculations for DNA and protein sequence alignments. Source code is publicly available for integration into C++ bioinformatics programs.

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Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

Pairwise local alignment is a critical tool for molecular biologists.
Accurate E-value calculation is essential for sequence alignment interpretation.
Existing methods may lack speed or flexibility for diverse alignment types.

Purpose of the Study:

To introduce efficient algorithms for calculating E-values in sequence alignment.
To provide tools for both standard local alignments and frameshifted alignments.
To enable widespread adoption and integration of these computational methods.

Main Methods:

Development of the Ascending Ladder Program (ALP) for rapid E-value calculation.
Development of the Frameshift Ascending Ladder Program (FALP) for frameshifted alignments.
Implementation of algorithms to handle arbitrary substitution matrices, gap costs, and letter abundances.

Main Results:

ALP achieves real-time E-value calculations (approx. 1 second) for protein-protein and DNA-DNA local alignments.
FALP offers similar E-value calculations for frameshifted DNA-protein alignments, albeit with slightly longer computation times.
C++ source codes for both ALP and FALP are publicly available.

Conclusions:

ALP and FALP offer significant computational efficiencies for sequence alignment E-value determination.
The availability of source code facilitates the direct implementation of these algorithms by C++ programmers.
These tools enhance the capabilities of molecular biologists and bioinformaticians.