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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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...
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...

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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

BioSAVE: display of scored annotation within a sequence context.

Richard F Pollock1, Boris Adryan

  • 1MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK. rfp26@mrc-lmb.cam.ac.uk

BMC Bioinformatics
|March 28, 2008
PubMed
Summary

BioSAVE is a new bioinformatics tool that allows users to dynamically visualize sequence annotations with adjustable score cutoffs. This dynamic visualization aids in biological interpretation and determining cutoff values for predicted features.

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Last Updated: Jul 6, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
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An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Sequence annotation visualization is crucial in bioinformatics.
  • Interpreting large datasets is challenging without score cutoffs.
  • Existing visualization tools often lack dynamic threshold adjustment.

Purpose of the Study:

  • To introduce BioSAVE, a novel sequence annotation viewer.
  • To provide on-the-fly threshold selection for visualization.
  • To enhance biological interpretation of sequence data.

Main Methods:

  • Developed BioSAVE as a versatile OS X application.
  • Implemented graphical display of sequence and annotation data.
  • Integrated on-the-fly controls for live customization of visualization thresholds.

Main Results:

  • BioSAVE enables dynamic visualization of scored features.
  • Supports various common file formats for sequence and annotation data.
  • Allows real-time adjustment of visualization thresholds for each feature.

Conclusions:

  • BioSAVE facilitates applications like visualizing transcription factor binding sites and structural domains.
  • Dynamic visualization aids in matching predicted features to experimental data.
  • The program, source code, and examples are freely available.