NDLI: GenoMosaic: on-demand multiple genome comparison and comparative annotation

Content Provider	IEEE Xplore Digital Library
Author	Gibas, C. Sturgill, D. Weller, J.
Copyright Year	2003
Description	Author affiliation: Virginia Tech, Blacksburg, VA, USA (Gibas, C.; Sturgill, D.)
Abstract	GenoMosaic is a portable database application for on demand multiple genome comparison. We discuss the methods used to generate a GenoMosaic data set from genome sequence data, and present the relational data model used in the application. We define an abstraction of genome sequence data (the feature mosaic) that allows us to bridge between annotation that describes features within single genes and that which includes possibly multiple genes and intergenic features over long stretches of genomic sequence. The goal of this project is to support new method development for on-demand multiple genome comparison. Each genome to be compared can be modeled as a string of generic features of any type that can be computationally defined, related by adjacency information within and among genomes. The generic feature abstraction makes it possible to study the arrangement of features in the genome at a level of detail which includes RNA genes, putative regulatory regions, SNPs, overlapping transcripts, intron splice junctions, alternative polyadenylation signals-in short, to incorporate significant sequence details which are not necessarily within protein-coding regions. This abstraction is amenable to functional implementation as a relational data model upon which novel query capabilities can be built, and provides objects that can be analyzed using algorithms for comparison of strings and lists. As an initial effort, we have implemented a prototype using a representative set of comparative and content-based annotation methods to reduce a collection of prokaryotic genomes to a feature mosaic representation. Entity-Relationship modeling was then used to develop a data model capable of storing detailed results, including complete parameters for each instance of analysis.
Sponsorship	IEEE Comput. Soc. Inf. Technol. Res. Inst. at Wright State Univ. IEEE Neural Networks Soc
Starting Page	158
Ending Page	165
File Size	320025
Page Count	8
File Format	PDF
ISBN	0769519075
DOI	10.1109/BIBE.2003.1188942
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2003-03-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Genomics Bioinformatics Data models Relational databases Spatial databases Bridges RNA Proteins Algorithm design and analysis Prototypes
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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