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Related Concept Videos

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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...
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Multi-species Conserved Sequences

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Related Experiment Video

Updated: Jun 4, 2026

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

Strategies for sequence similarity database searches.

David W Mount

    CSH Protocols
    |March 2, 2011
    PubMed
    Summary

    Screening large database search outputs is challenging. This article details simple procedures to limit sequence output, improving the assessment of remote sequence similarity in bioinformatics.

    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • Database similarity searches generate extensive results.
    • Assessing the relevance of distantly related sequences in large outputs is difficult.
    • Efficiently managing and interpreting search results is crucial for biological research.

    Purpose of the Study:

    • To provide practical methods for limiting the output of database similarity search programs.
    • To enhance the ability of researchers to screen and assess sequence similarity results.
    • To offer strategies for optimizing protein sequence database searches.

    Main Methods:

    • Limiting searches to curated protein sequence databases like SwissProt and PIR.
    • Focusing searches on specific genomes instead of comprehensive translated databases (e.g., GenPept).

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    Last Updated: Jun 4, 2026

    The ITS2 Database
    16:17

    The ITS2 Database

    Published on: March 12, 2012

    Novel Sequence Discovery by Subtractive Genomics
    09:40

    Novel Sequence Discovery by Subtractive Genomics

    Published on: January 25, 2019

    Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
    07:49

    Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

    Published on: August 16, 2017

  • Implementing program-specific procedures to reduce redundant alignments.

    • Main Results:

    • Reduced volume of search results.
    • Improved focus on relevant sequence alignments.
    • More efficient screening of remotely related sequences.

    Conclusions:

    • Implementing output limitation strategies significantly improves the manageability of database search results.
    • Utilizing curated databases and specific genome searches enhances the quality and relevance of similarity assessments.
    • Simple procedural adjustments can optimize the interpretation of sequence similarity data in bioinformatics.