Related Experiment Video
Updated: Dec 31, 2025
07:49
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
7.4K
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments
Dariusz Przybylski1, Burkhard Rost
1Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. dsp23@columbia.edu
Nucleic Acids Research
|March 21, 2007
Summary
This study introduces a novel consensus sequence method that enhances protein sequence alignment searches. The approach improves the accuracy of identifying distant protein relationships without altering existing software.
Area of Science:
- Computational biology
- Bioinformatics
- Genomics
Background:
- Sequence alignments are fundamental in molecular biology.
- Current methods like BLAST and PSI-BLAST have limitations in speed and complexity for profile-profile comparisons.
- Consensus sequences represent gene families by identifying the most frequent nucleic or amino acid at each position.
Purpose of the Study:
- To develop a novel approach for consensus-sequence-based comparisons.
- To enhance the performance of existing sequence alignment tools, specifically PSI-BLAST.
- To improve the identification of distant structural relations and alignments between proteins.
Main Methods:
- A novel consensus-sequence-based comparison method was developed.
- This method was implemented as an add-on to PSI-BLAST without code modification.
- The approach was tested for its effectiveness in identifying sequence relatedness and structural relationships.
Main Results:
- The consensus sequence add-on significantly improved searches and alignments within PSI-BLAST.
- Improvements were particularly notable for challenging tasks, including identifying distant protein structural relations.
- Consistent improvements were observed even at high accuracy/low error rates for non-trivially related proteins.
Conclusions:
- The consensus sequence approach offers a simple yet effective enhancement to PSI-BLAST.
- This method requires minimal computational overhead and no alteration to existing software.
- The technique is readily applicable for advanced users and available online.
Related Concept Videos
02:51Multi-species Conserved Sequences
4.6K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.6K
01:49Conserved Binding Sites
5.0K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.0K