Date of Award

Fall 2018

Document Type

Thesis

Degree Name

Master of Science in Bioinformatics - (M.S.)

Department

Computer Science

First Advisor

Tian, Bin

Second Advisor

Roshan, Usman W.

Third Advisor

Wei, Zhi

Abstract

Polyadenation is an important process occurring in the messenger RNA that involves cleavage of 3 end nascent mRNAs and addition of poly(A) tails. For this thesis,I present PolyA DB3 ,a database cataloging cleavage and polyadenylation sites (PASs) in several genomes specifically for human,mouse,rat and chicken. This database is based on deep sequencing data. PASs are mapped by the 3’ region extraction and deep sequencing (3’READS) method, ensuring unequivocal PAS identification. Large volume of data based on diverse biological samples is used to increase PAS coverage and provide PAS usage information. Strand-specific RNA-seq data were used to extend annotated 3’ ends of genes to obtain more thorough annotations of alternative polyadenylation (APA) sites. The database also has information regarding conservation of PAS between these species. Similar analysis has also been done on the PASs identified from frog samples and the identification of conservation of the PASs.

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