Related Experiment Video
Updated: Apr 20, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
DivA: detection of non-homologous and very divergent regions in protein sequence alignments
Marie Lisandra Zepeda Mendoza, Sanne Nygaard, Rute R da Fonseca1
1Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark. rute.r.da.fonseca@gmail.com.
Background:
Sequence alignments are used to find evidence of homology but sometimes contain regions that are difficult to align which can interfere with the quality of the subsequent analyses. Although it is possible to remove problematic regions manually, this is non-practical in large genome scale studies, and the results suffer from irreproducibility arising from subjectivity. Some automated alignment trimming methods have been developed to remove problematic regions in alignments but these mostly act by removing complete columns or complete sequences from the MSA, discarding a lot of informative sites.
Findings:
Here we present a tool that identifies Divergent windows in protein sequence Alignments (DivA). DivA makes no assumptions on evolutionary models, and it is ideal for detecting incorrectly annotated segments within individual gene sequences. DivA works with a sliding-window approach to estimate four divergence-based parameters and their outlier values. It then classifies a window of a sequence of an alignment as very divergent (potentially non-homologous) if it presents a combination of outlier values for the four parameters it calculates. The windows classified as very divergent can optionally be masked in the alignment.
Conclusions:
DivA automatically identifies very divergent and incorrectly annotated genic regions in MSAs avoiding the subjective and time-consuming problem of manual annotation. The output is clear to interpret and allows the user to take more informed decisions for reducing the amount of sequence discarded but still finding the potentially erroneous and non-homologous regions.
More Related Videos
07:08Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
16:02Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
Published on: February 10, 2023
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Conservation of Protein Domains
Conserved Binding Sites
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...
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...