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Related Concept Videos

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.
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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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

Software tool for researching annotations of proteins: open-source protein annotation software with data

Vivek N Bhatia1, David H Perlman, Catherine E Costello

  • 1Cardiovascular Proteomics Center, Boston University School of Medicine, 670 Albany Street, Room 504, Boston, Massachusetts 02118, USA.

Analytical Chemistry
|October 21, 2009
PubMed
Summary
This summary is machine-generated.

Researchers can now accelerate proteomics data analysis with STRAP, a free software tool. STRAP automates protein annotation and visualization, integrating Gene Ontology terms for enhanced biological insights.

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Published on: April 11, 2019

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Interpreting proteomics data requires extensive annotation, including protein functions and interactions.
  • Manual data compilation from online databases is time-consuming and requires expert input.
  • Limited availability of user-friendly tools hinders the visualization and interpretation of large proteomics datasets.

Purpose of the Study:

  • To develop a software tool that automates the annotation and visualization of proteomics data.
  • To accelerate biological research by simplifying the interpretation of mass spectrometry results.
  • To provide researchers with an accessible, open-source solution for proteomics data analysis.

Main Methods:

  • Developed Software Tool for Researching Annotations of Proteins (STRAP), a C# application.
  • STRAP automatically retrieves Gene Ontology (GO) terms from UniProtKB and EBI GOA databases.
  • Implemented features for tabular summaries, user editing, graphical visualizations (pie and bar charts), FASTA export, and Gaggle microformat encoding.

Main Results:

  • STRAP provides automated annotation of proteomics IDs with GO terms and associated meta-information.
  • Results are presented in an interactive tabular format with sortable views.
  • Graphical representations (pie and bar charts) aid in the interpretation of biological processes, cellular components, and molecular functions.
  • Export options for FASTA files and Gaggle microformat facilitate further analysis and re-searching.

Conclusions:

  • STRAP offers a user-friendly, open-source solution for automating proteomics data annotation and visualization.
  • The tool enhances the derivation of biological meaning and the building of testable hypotheses from proteomics experiments.
  • STRAP accelerates research by streamlining data interpretation and enabling deeper analysis through integrated features.