Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

Thumbnail image of item number 1 in: 'Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology'.
Thumbnail image of item number 2 in: 'Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology'.
Thumbnail image of item number 3 in: 'Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology'.
Thumbnail image of item number 4 in: 'Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology'.
Showing 1-4 of 104 pages in this document.

PDF Version Also Available for Download.

Description

This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese`s group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group … continued below

Physical Description

101 p.

Creation Information

Taylor, R. C. November 1, 1991.

Context

This thesis or dissertation is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided by the UNT Libraries Government Documents Department to the UNT Digital Library, a digital repository hosted by the UNT Libraries. It has been viewed 89 times. More information about this document can be viewed below.

Who

People and organizations associated with either the creation of this thesis or dissertation or its content.

Author

Sponsor

Publisher

Provided By

UNT Libraries Government Documents Department

Serving as both a federal and a state depository library, the UNT Libraries Government Documents Department maintains millions of items in a variety of formats. The department is a member of the FDLP Content Partnerships Program and an Affiliated Archive of the National Archives.

About | Browse this Partner

Contact Us

Corrections Questions

What

Descriptive information to help identify this thesis or dissertation. Follow the links below to find similar items on the Digital Library.

Description

This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese`s group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

Physical Description

101 p.

Notes

OSTI; NTIS; GPO Dep.

Source

  • Other Information: DN: Thesis submitted to Case Western Reserve University, Cleveland, OH; TH: Thesis (M.S.)

Language

Item Type

Identifier

Unique identifying numbers for this document in the Digital Library or other systems.

  • Other: DE92004954
  • Report No.: ANL--91/29
  • Grant Number: W-31109-ENG-38
  • Office of Scientific & Technical Information Report Number: 10108317
  • Archival Resource Key: ark:/67531/metadc1273380

Collections

This document is part of the following collection of related materials.

Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

About | Browse this Collection

What responsibilities do I have when using this thesis or dissertation?

Digital Files

When

Dates and time periods associated with this thesis or dissertation.

Creation Date

  • November 1, 1991

Added to The UNT Digital Library

  • Oct. 12, 2018, 6:44 a.m.

Description Last Updated

  • Nov. 21, 2018, 2:36 p.m.

Usage Statistics

When was this document last used?

Yesterday: 0
Past 30 days: 0
Total Uses: 89
More Statistics

Interact With This Thesis Or Dissertation

Here are some suggestions for what to do next.

Start Reading

Thumbnail image of item number 1 in: 'Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology'.
Thumbnail image of item number 2 in: 'Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology'.
Thumbnail image of item number 3 in: 'Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology'.
Thumbnail image of item number 4 in: 'Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology'.

PDF Version Also Available for Download.

Citations, Rights, Re-Use

International Image Interoperability Framework

IIF Logo

We support the IIIF Presentation API

Links for Robots

Helpful links in machine-readable formats.

Archival Resource Key (ARK)

International Image Interoperability Framework (IIIF)

Metadata Formats

Images

URLs

Stats

Taylor, R. C. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology, thesis or dissertation, November 1, 1991; Illinois. (https://digital.library.unt.edu/ark:/67531/metadc1273380/: accessed May 17, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.

Back to Top of Screen