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Related Concept Videos

Multiple Comparison Tests01:13

Multiple Comparison Tests

Multiple comparison test, abbreviated as MCT, is a post hoc analysis generally performed after comparing multiple samples with one or more tests. An MCT will help identify a significantly different sample among multiple samples or a factor among multiple factors.
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Archival Research

Some researchers gain access to large amounts of data without interacting with a single research participant. Instead, they use existing records to answer various research questions. This type of research approach is known as archival research. Archival research relies on looking at past records or data sets to look for interesting patterns or relationships. For example, a researcher might access the academic records of all individuals who enrolled in college within the past ten years and...
Statistical Analysis: Overview01:11

Statistical Analysis: Overview

When we take repeated measurements on the same or replicated samples, we will observe inconsistencies in the magnitude. These inconsistencies are called errors. To categorize and characterize these results and their errors, the researcher can use statistical analysis to determine the quality of the measurements and/or suitability of the methods.
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Comparison Tests

An infinite series composed of positive terms may either approach a finite value or increase without bound. Determining which outcome occurs is a central task in calculus, and comparison tests provide structured methods for making this determination. Rather than evaluating a series directly, these tests relate it to another series whose behavior is already known, allowing conclusions to be drawn through logical comparison.The direct comparison test applies to series with positive terms. If each...
Chi-square Analysis02:46

Chi-square Analysis

The chi-square test is a statistical hypothesis test. It is used to check whether there is a significant difference between an expected value and an observed value. In the context of genetics, it enables us to either accept or reject a hypothesis, based on how much the observed values deviate from the expected values.
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Statistical Analysis System (SAS)01:14

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SAS, short for Statistical Analysis System, is a powerful data analysis, management, and visualization tool. Developed by the SAS Institute in the early 1970s, SAS has evolved into a comprehensive software suite used across various industries for statistical analysis, business intelligence, and predictive modeling.
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Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases
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COPS benchmark: interactive analysis of database search methods.

Karl Frank1, Markus Gruber, Manfred J Sippl

  • 1Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria.

Bioinformatics (Oxford, England)
|January 19, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a new web service for evaluating protein sequence alignment methods using a specialized dataset for receiver operating characteristic (ROC) analysis. It offers detailed insights into alignment quality and facilitates fair comparisons between different search tools.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Receiver operating characteristic (ROC) analysis is standard for evaluating sequence database search methods.
  • Accurate ROC analysis requires datasets with consistent true positives and true negatives per query.
  • Existing datasets may not be optimally designed for rigorous alignment quality assessment.

Purpose of the Study:

  • To present a novel web service for ROC analysis of sequence alignment methods.
  • To introduce a specialized dataset derived from protein structure classification (COPS) for improved ROC analysis.
  • To enable detailed investigation and comparison of alignment quality.

Main Methods:

  • Development of a web service with an intuitive interface.
  • Creation of a dataset based on the quantitative classification of protein structures (COPS).
  • Implementation of analysis features including false positives per query and structural similarity visualization.

Main Results:

  • The web service provides detailed performance metrics for sequence alignment methods.
  • It allows for direct comparison of a specific method against popular standard methods.
  • Visualization aids in understanding the structural basis of alignment quality.

Conclusions:

  • The novel web service and dataset enhance the reliability of ROC analysis for sequence search methods.
  • It facilitates a more accurate and fair comparison of different alignment algorithms.
  • The tool aids in the investigation of alignment quality by linking sequence similarity to structural information.