Tools and Training for Genome Annotation and Analysis

Update item information
Publication Type dissertation
School or College School of Medicine
Department Human Genetics
Author Campbell, Michael Stephen
Title Tools and Training for Genome Annotation and Analysis
Date 2015-12
Description The MAKER genome annotation and curation software tool was developed in response to increased demand for genome annotation services, secondary to decreased genome sequencing costs. MAKER currently has over 1000 registered users throughout the world. This wide adoption of MAKER has uncovered the need for additional functionalities. Here I addressed moving MAKER into the domain of plant annotation, expanding MAKER to include new methods of gene and noncoding RNA annotation, and improving usability of MAKER through documentation and community outreach. To move MAKER into the plant annotation domain, I benchmarked MAKER on the well-annotated Arabidopsis thaliana genome. MAKER performs well on the Arabidopsis genome in de novo genome annotation and was able to improve the current TAIR10 gene models by incorporating mRNA-seq data not available during the original annotation efforts. In addition to this benchmarking, I annotated the genome of the sacred lotus Nelumbo Nucifera. I enabled noncoding RNA annotation in MAKER by adding the ability for MAKER to run and process the outputs of tRNAscan-SE and snoscan. These functionalities were tested on the Arabidopsis genome and used MAKER to annotate tRNAs and snoRNAs in Zea mays. The resulting version of MAKER was named MAKER-P. I added the functionality of a combiner by adding EVidence Modeler to the MAKER code base. iv As the number of MAKER users has grown, so have the help requests sent to the MAKER developers list. Motivated by the belief that improving the MAKER documentation would obviate the need for many of these requests, I created a media wiki that was linked to the MAKER download page, and the MAKER developers list was made searchable. Additionally I have written a unit on genome annotation using MAKER for Current Protocols in Bioinformatics. In response to these efforts I have seen a corresponding decrease in help requests, even though the number of registered MAKER users continues to increase. Taken together these products and activities have moved MAKER into the domain of plant annotation, expanded MAKER to include new methods of gene and noncoding RNA annotation, and improved the usability of MAKER through documentation and community outreach.
Type Text
Publisher University of Utah
Subject MESH Molecular Sequence Annotation; Software; Documentation; Quality Control; Sensitivity and Specificity; Benchmarking; Genome; Genome, Plant; Arabidopsis; Nelumbo
Dissertation Institution University of Utah
Dissertation Name Doctor of Philosophy
Language eng
Relation is Version of Digital version of Tools and Training for Genome Annotation and Analysis
Rights Management Copyright © Michael Stephen Campbell 2015
Format Medium applicationb/pdf
Format Extent 7,707,980 bytes
Source Original in Marriott Library Special Collections
ARK ark:/87278/s635344r
Setname ir_etd
Date Created 2019-07-30
Date Modified 2021-05-06
ID 1432963
Reference URL https://collections.lib.utah.edu/ark:/87278/s635344r
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