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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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 DNA...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Related Experiment Video

Updated: Jun 25, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Sequence context-specific profiles for homology searching.

A Biegert1, J Söding

  • 1Gene Center Munich and Ludwig Maximilian University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

Proceedings of the National Academy of Sciences of the United States of America
|February 24, 2009
PubMed
Summary

Context-specific amino acid similarities improve protein sequence alignment and database searching. This new method (CS-BLAST) enhances sensitivity over 2-fold without sacrificing speed, advancing biological sequence comparison.

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Last Updated: Jun 25, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
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Published on: July 12, 2022

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10:44

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Protein function inference relies on homologous sequences.
  • Current sequence comparison uses substitution matrices lacking local context.
  • Local sequence context is crucial for understanding mutations.

Purpose of the Study:

  • To develop context-specific amino acid similarities for improved sequence analysis.
  • To enhance the sensitivity and quality of sequence alignment and database searching.
  • To create a generalizable paradigm for biological sequence comparison.

Main Methods:

  • Deriving context-specific amino acid similarities from local sequence windows.
  • Integrating context-specific similarities into NCBI BLAST (CS-BLAST).
  • Applying the context-specific paradigm to sequence profiles (CSI-BLAST).

Main Results:

  • Sequence context provides more information on mutations than individual residues.
  • CS-BLAST achieves over 2-fold sensitivity increase on benchmark sets without speed loss.
  • CSI-BLAST outperforms standard PSI-BLAST in sensitivity and efficiency.

Conclusions:

  • Context-specific similarities offer a significant advancement over traditional methods.
  • The CS-BLAST approach enhances alignment quality and search sensitivity.
  • This paradigm is broadly applicable to protein and nucleotide sequence analysis.