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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Aligning short reads to reference alignments and trees.

Simon A Berger¹, Alexandros Stamatakis

¹The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, D-69118 Heidelberg, Germany. simon.berger@h-its.org

Bioinformatics (Oxford, England)

|June 4, 2011

Summary

This summary is machine-generated.

We developed a new phylogeny-aware alignment method to accurately place short metagenomic reads onto reference phylogenies. This approach improves read alignment accuracy significantly compared to existing methods.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Likelihood-based methods for placing short metagenomic reads into reference phylogenies are emerging.
Current methods lack clarity on aligning reads to reference alignments used for phylogeny inference.
The adaptability and utility of reference phylogenies for improving read alignment accuracy remain unexplored.

Purpose of the Study:

To assess different short read alignment strategies for metagenomic data.
To propose and evaluate a novel phylogeny-aware alignment procedure.
To determine if reference phylogenies can enhance read alignment accuracy.

Main Methods:

Assessed various short read alignment strategies.
Developed a novel phylogeny-aware alignment procedure.
Evaluated alignment accuracy against phylogeny-agnostic methods.

Main Results:

The proposed phylogeny-aware alignment method significantly improves read alignment accuracy.
Accuracy gains of up to 5.8 times were observed compared to phylogeny-agnostic methods.
The method is adaptable to reads aligned using different strategies (e.g., PRANK(+F), MUSCLE).

Conclusions:

Phylogeny-aware alignment is crucial for accurate metagenomic read placement.
The novel method offers substantial improvements in alignment accuracy.
This approach enhances the utility of reference phylogenies in metagenomic analysis.