Biology subjects

Roddy, J. W.

Publications and source records attributed to Roddy, J. W..

3 recordsLinked to original sources

bioRxiv2024

nail: software for high-speed, high-sensitivity protein sequence annotation

Fast is fine, but accuracy is final. --Wyatt Earp BackgroundProfile hidden Markov models (pHMMs) deliver state-of-the-art sensitivity for sequence annotation, but the Forward/Backward algorithm fills a dynamic programming matrix sized by the product of model and sequence lengths, making pHMM search slower than fast heuristic alignment tools like MMseqs2 by an order of magnitude or more. ResultsWe introduce nail, which approximates Forward/Backward by computing only a sparse cloud of high-probability matrix cells, recovering accurate pHMM scores, E-values, and alignments at a fraction of the cost. nail annotates the ~2.4 billion protein MGnify metagenomic dataset with all of Pfam in 73.9 hours on a single 48 core machine, recovering nearly all of HMMERs recall advantage over MMseqs2, with run time ~8.7x faster than HMMER3. Detailed analysis of HMMER-only multi-domain hits suggests that many of these matches missed by nail are the result of accumulating score across short, often fragmentary alignments to repetitive regions of the target, consistent with spurious hits rather than genuine homology. We also derive a closed-form approximation for single-sequence E-value calibration, eliminating a per-model simulation step. nail is released under the open BSD-3-clause license at https://github.com/TravisWheelerLab/nail.

bioinformatics↗

bioRxiv2023

VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes

Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists, and have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES, a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster, and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1,072 Pseudomonas spp. genomes. VIBES software is available at https://github.com/TravisWheelerLab/VIBES.

bioinformatics↗

bioRxiv2021

PolyA: a tool for adjudicating competing annotations of biological sequences

Annotation of a biological sequence is usually performed by aligning that sequence to a database of known sequence elements. When that database contains elements that are highly similar to each other, the proper annotation may be ambiguous, because several entries in the database produce high-scoring alignments. Typical annotation methods work by assigning a label based on the candidate annotation with the highest alignment score; this can overstate annotation certainty, mislabel boundaries, and fails to identify large scale rearrangements or insertions within the annotated sequence. Here, we present a new software tool, PolyA, that adjudicates between competing alignment-based annotations by computing estimates of annotation confidence, identifying a trace with maximal confidence, and recursively splicing/stitching inserted elements. PolyA communicates annotation certainty, identifies large scale rearrangements, and detects boundaries between neighboring elements.

bioinformatics↗