• Skip to main content
  • Skip to primary sidebar
AAAI

AAAI

Association for the Advancement of Artificial Intelligence

    • AAAI

      AAAI

      Association for the Advancement of Artificial Intelligence

  • About AAAIAbout AAAI
    • AAAI Officers and Committees
    • AAAI Staff
    • Bylaws of AAAI
    • AAAI Awards
      • Fellows Program
      • Classic Paper Award
      • Dissertation Award
      • Distinguished Service Award
      • Allen Newell Award
      • Outstanding Paper Award
      • Award for Artificial Intelligence for the Benefit of Humanity
      • Feigenbaum Prize
      • Patrick Henry Winston Outstanding Educator Award
      • Engelmore Award
      • AAAI ISEF Awards
      • Senior Member Status
      • Conference Awards
    • AAAI Resources
    • AAAI Mailing Lists
    • Past AAAI Presidential Addresses
    • Presidential Panel on Long-Term AI Futures
    • Past AAAI Policy Reports
      • A Report to ARPA on Twenty-First Century Intelligent Systems
      • The Role of Intelligent Systems in the National Information Infrastructure
    • AAAI Logos
    • News
  • aaai-icon_ethics-diversity-line-yellowEthics & Diversity
  • Conference talk bubbleConferences & Symposia
    • AAAI Conference
    • AIES AAAI/ACM
    • AIIDE
    • IAAI
    • ICWSM
    • HCOMP
    • Spring Symposia
    • Summer Symposia
    • Fall Symposia
    • Code of Conduct for Conferences and Events
  • PublicationsPublications
    • AAAI Press
    • AI Magazine
    • Conference Proceedings
    • AAAI Publication Policies & Guidelines
    • Request to Reproduce Copyrighted Materials
  • aaai-icon_ai-magazine-line-yellowAI Magazine
    • Issues and Articles
    • Author Guidelines
    • Editorial Focus
  • MembershipMembership
    • Member Login
    • Developing Country List
    • AAAI Chapter Program

  • Career CenterCareer Center
  • aaai-icon_ai-topics-line-yellowAITopics
  • aaai-icon_contact-line-yellowContact

Home / Proceedings / Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology / Book One

GeneQuiz: A Workbench for Sequence Analysis

March 15, 2023

Download PDF

Authors

Michael Scharf

Reinheard Schneider

Georg Casari

Peer Bork

Alfonso Valencia

Christos Ouzounis

and Chris Sander

DOI:


Abstract:

We present the prototype of a software system, cMled GeneQuiz, for large-scale biological sequence analysis. The system was designed to meet the needs that arise in computational sequence analysis and our past experience with the analysis of 171 protein sequences of yeast chromosome III. We explain the cognitive chMlenges associated with this particular research activity and present, our model of the sequence analysis process. The prototype system consists of two parts: (i) the database update and search system (driven by perl programs and rdb, a simple relational database engine also written in perl) and (ii) the visualization and browsing system (developed under C++/ET++). The principal design requirement for the first paxt was the complete automation of all repetitive actions: database updates, efficient sequence similarity searches and sampling of results in a uniform fashion. Thc user is then presented with "hit-lists" that summarize the results from heterogeneous database searches. The expert’s primary task now simply becomes the further analysis of the candidate entries, where the problem is to extract adequate information about functional characteristics of the query protein rapidly. This second task is tremendously accelerated by a simple combination of the heterogeneous output into uniform relational tables and the provision of browsing mechanisms that give access to database records, sequence entries and alignment views. Indexing of molecular sequence databases provides fast retrieval of individuM entries with the use of unique identifiers as well as browsing through databases using pre-existing cross-references. The presentation here covers an overview of the architecture of the system prototype and our experiences on its applicability in sequence analysis. The utility of Genequiz has been already proven during the analysis of 331 protein sequences from yeast chromosome XI and a quarter of the Mycoplasma capricolum genome, containing 314 proteins. Further developments will allow active guidance of the user by a rule-based system. Also, dependencies will be minimized so that the system can be made publicly available.

Topics: ISMB

Primary Sidebar

HOW TO CITE:

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander GeneQuiz: A Workbench for Sequence Analysis Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology (1994) .

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander GeneQuiz: A Workbench for Sequence Analysis ISMB 1994, .

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander (1994). GeneQuiz: A Workbench for Sequence Analysis. Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology, .

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander. GeneQuiz: A Workbench for Sequence Analysis. Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology 1994 p..

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander. 1994. GeneQuiz: A Workbench for Sequence Analysis. "Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology". .

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander. (1994) "GeneQuiz: A Workbench for Sequence Analysis", Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology, p.

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander, "GeneQuiz: A Workbench for Sequence Analysis", ISMB, p., 1994.

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander. "GeneQuiz: A Workbench for Sequence Analysis". Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology, 1994, p..

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander. "GeneQuiz: A Workbench for Sequence Analysis". Proceedings Of The Second International Conference On Intelligent Systems For Molecular Biology, (1994): .

Michael Scharf||Reinheard Schneider||Georg Casari||Peer Bork||Alfonso Valencia||Christos Ouzounis||and Chris Sander. GeneQuiz: A Workbench for Sequence Analysis. ISMB[Internet]. 1994[cited 2023]; .


ISSN:


Published by AAAI Press, Palo Alto, California USA
Copyright 2022, Association for the Advancement of
Artificial Intelligence 1900 Embarcadero Road, Suite
101, Palo Alto, California 94303 All Rights Reserved

We use cookies on our website to give you the most relevant experience by remembering your preferences and repeat visits. By clicking “Accept All”, you consent to the use of ALL the cookies. However, you may visit "Cookie Settings" to provide a controlled consent.
Cookie SettingsAccept All
Manage consent

Privacy Overview

This website uses cookies to improve your experience while you navigate through the website. Out of these, the cookies that are categorized as necessary are stored on your browser as they are essential for the working of basic functionalities of the website. We also use third-party cookies that help us analyze and understand how you use this website. These cookies will be stored in your browser only with your consent. You also have the option to opt-out of these cookies. But opting out of some of these cookies may affect your browsing experience.
Necessary
Always Enabled
Necessary cookies are absolutely essential for the website to function properly. These cookies ensure basic functionalities and security features of the website, anonymously.
CookieDurationDescription
cookielawinfo-checkbox-analytics11 monthsThis cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Analytics".
cookielawinfo-checkbox-functional11 monthsThe cookie is set by GDPR cookie consent to record the user consent for the cookies in the category "Functional".
cookielawinfo-checkbox-necessary11 monthsThis cookie is set by GDPR Cookie Consent plugin. The cookies is used to store the user consent for the cookies in the category "Necessary".
cookielawinfo-checkbox-others11 monthsThis cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Other.
cookielawinfo-checkbox-performance11 monthsThis cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Performance".
viewed_cookie_policy11 monthsThe cookie is set by the GDPR Cookie Consent plugin and is used to store whether or not user has consented to the use of cookies. It does not store any personal data.
Functional
Functional cookies help to perform certain functionalities like sharing the content of the website on social media platforms, collect feedbacks, and other third-party features.
Performance
Performance cookies are used to understand and analyze the key performance indexes of the website which helps in delivering a better user experience for the visitors.
Analytics
Analytical cookies are used to understand how visitors interact with the website. These cookies help provide information on metrics the number of visitors, bounce rate, traffic source, etc.
Advertisement
Advertisement cookies are used to provide visitors with relevant ads and marketing campaigns. These cookies track visitors across websites and collect information to provide customized ads.
Others
Other uncategorized cookies are those that are being analyzed and have not been classified into a category as yet.
SAVE & ACCEPT