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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Profile Comparer: a program for scoring and aligning profile hidden Markov models.

Martin Madera¹

¹Department of Computer Science, University of Bristol, Bristol, UK. martin.madera@gmail.com

Bioinformatics (Oxford, England)

|October 11, 2008

Summary

This summary is machine-generated.

Profile Comparer (PRC) is a new tool for scoring and aligning protein family profile hidden Markov models (HMMs). It supports various popular HMM packages and PSI-BLAST checkpoint files, offering a flexible solution for bioinformatics analysis.

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Area of Science:

Bioinformatics
Computational Biology
Structural Bioinformatics

Background:

Profile hidden Markov models (HMMs) are crucial for protein family analysis.
Existing tools like SAM and HMMER generate popular profile HMMs.
PSI-BLAST checkpoint files also represent valuable protein sequence profile data.

Purpose of the Study:

To introduce Profile Comparer (PRC), a novel standalone program.
To describe the underlying profile-profile algorithm implemented in PRC.
To provide a tool for scoring and aligning diverse profile HMMs.

Main Methods:

PRC implements a profile-profile comparison algorithm.
The program is capable of reading HMMs from SAM and HMMER.
It also supports the ingestion of PSI-BLAST checkpoint files.

Main Results:

PRC offers a unified platform for comparing different profile HMMs.
The tool facilitates the scoring and alignment of protein family profiles.
Demonstrates compatibility with established bioinformatics tools.

Conclusions:

PRC provides a valuable addition to the bioinformatics toolkit.
The program enhances the analysis of protein families through profile comparisons.
Availability of source code and binaries promotes wider adoption and research.