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

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.
Authors:
Publication Date:
OSTI Identifier:
6057182
Report Number(s):
ANL-91/29
ON: DE92004954
DOE Contract Number:
W-31109-ENG-38
Resource Type:
Technical Report
Resource Relation:
Other Information: Thesis (M.S.). Thesis submitted to Case Western Reserve University, Cleveland, OH
Research Org:
Argonne National Lab., IL (United States)
Sponsoring Org:
DOE; USDOE, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; RNA; TEXT EDITORS; AUTOMATION; COMPUTER CODES; MOLECULAR BIOLOGY; PROLOG; NUCLEIC ACIDS; ORGANIC COMPOUNDS; PROGRAMMING LANGUAGES 550200* -- Biochemistry; 990200 -- Mathematics & Computers