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Related Concept Videos

Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
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...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Convergent Evolution01:54

Convergent Evolution

Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.The structures that arise from convergent evolution are called analogous structures. They are similar in function even if they are dissimilar in structure. Further, structures can be analogous while also...

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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

Inferring function from homology.

Richard D Emes1

  • 1Department of Biology, University College London, London, United Kingdom.

Methods in Molecular Biology (Clifton, N.J.)
|August 21, 2008
PubMed
Summary
This summary is machine-generated.

Bioinformatics tools can infer protein function from DNA sequences when experimental methods are unfeasible. This pipeline uses web-based tools to analyze unknown gene functions, generating testable hypotheses.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Modern molecular biology generates vast amounts of biological sequence data.
  • Experimental determination of protein function is often impractical for large datasets or uncharacterized genes.
  • Bioinformatics offers a complementary approach to infer gene and protein function.

Purpose of the Study:

  • To present a pipeline of freely available web-based tools for analyzing protein-coding DNA sequences of unknown function.
  • To enable the inference of gene function through computational methods.
  • To guide the generation of testable hypotheses for protein function.

Main Methods:

  • Utilizing a pipeline of web-based bioinformatics tools.
  • Employing sequence similarity methods for homologue detection, including BLAST and PSI-BLAST.
  • Annotating protein function via protein domain detection using SMART and Pfam.
  • Comparing results with whole genome data.

Main Results:

  • The pipeline facilitates the analysis of protein-coding DNA sequences with unknown functions.
  • Information gathered at each step contributes to formulating functional hypotheses.
  • Sequence similarity and domain detection methods are key components for function inference.
  • Integration with whole genome data enhances functional predictions.

Conclusions:

  • A bioinformatics pipeline can effectively analyze DNA sequences of unknown function.
  • This approach aids in generating testable hypotheses for protein function.
  • Freely available web tools provide accessible methods for functional genomics research.
  • Computational analysis is crucial for managing and interpreting large-scale biological data.