Assessing the discordance of multiple sequence alignments
Related Experiment Video
Updated: Jun 19, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
Published on: February 10, 2023
1Biomarker Research Initiative in Mass Spectrometry Center, Thermo, 790 Memorial Drive, Suite 201, Cambridge, MA 02139, USA. amol.prakash@thermofisher.com
Abstract:
Multiple sequence alignments have wide applicability in many areas of computational biology, including comparative genomics, functional annotation of proteins, gene finding, and modeling evolutionary processes. Because of the computational difficulty of multiple sequence alignment and the availability of numerous tools, it is critical to be able to assess the reliability of multiple alignments. We present a tool called StatSigMA to assess whether multiple alignments of nucleotide or amino acid sequences are contaminated with one or more unrelated sequences. There are numerous applications for which StatSigMA can be used. Two such applications are to distinguish homologous sequences from nonhomologous ones and to compare alignments produced by various multiple alignment tools. We present examples of both types of applications.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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 form...
Kendall's Coefficient of Concordance
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

