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Updated: May 26, 2026

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

Hobbes: optimized gram-based methods for efficient read alignment.

Athena Ahmadi¹, Alexander Behm, Nagesh Honnalli

¹Department of Computer Science, University of California, Irvine, CA 92697, USA.

Nucleic Acids Research

|December 27, 2011

Summary

Hobbes is a new program for mapping short DNA reads to reference genomes. It offers significant speed improvements over existing tools while maintaining high accuracy for read alignment.

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Area of Science:

Genomics
Bioinformatics

Background:

High-throughput sequencing generates vast amounts of data requiring efficient read mapping.
Mapping short reads to large reference genomes presents computational challenges due to data volume and approximate matches.

Purpose of the Study:

Introduce Hobbes, a novel gram-based program for efficient short read alignment.
Improve read mapping performance and accuracy for genomic applications.

Main Methods:

Developed Hobbes utilizing an optimized k-mer selection and a cache-efficient pruning filter.
Supported both Hamming and edit distance for read mapping.
Tested performance on real and simulated data (35-100 bp reads).

Main Results:

Hobbes demonstrated superior speed compared to state-of-the-art programs like Bowtie and BWA.
Achieved approximately 5x speedup over Bowtie and 2-10x over BWA.
Maintained high mapping quality across various read lengths and error rates.

Conclusions:

Hobbes offers a substantial performance enhancement for short read mapping.
The program is publicly available and supports the SAM output format, facilitating integration into existing bioinformatics pipelines.