Chapter title |
Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center
|
---|---|
Chapter number | 4 |
Book title |
Comparative Genomics
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-7463-4_4 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7461-0, 978-1-4939-7463-4
|
Authors |
Alice R. Wattam, Thomas Brettin, James J. Davis, Svetlana Gerdes, Ronald Kenyon, Dustin Machi, Chunhong Mao, Robert Olson, Ross Overbeek, Gordon D. Pusch, Maulik P. Shukla, Rick Stevens, Veronika Vonstein, Andrew Warren, Fangfang Xia, Hyunseung Yoo, Wattam, Alice R., Brettin, Thomas, Davis, James J., Gerdes, Svetlana, Kenyon, Ronald, Machi, Dustin, Mao, Chunhong, Olson, Robert, Overbeek, Ross, Pusch, Gordon D., Shukla, Maulik P., Stevens, Rick, Vonstein, Veronika, Warren, Andrew, Xia, Fangfang, Yoo, Hyunseung |
Abstract |
In the "big data" era, research biologists are faced with analyzing new types that usually require some level of computational expertise. A number of programs and pipelines exist, but acquiring the expertise to run them, and then understanding the output can be a challenge.The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org ) has created an end-to-end analysis platform that allows researchers to take their raw reads, assemble a genome, annotate it, and then use a suite of user-friendly tools to compare it to any public data that is available in the repository. With close to 113,000 bacterial and more than 1000 archaeal genomes, PATRIC creates a unique research experience with "virtual integration" of private and public data. PATRIC contains many diverse tools and functionalities to explore both genome-scale and gene expression data, but the main focus of this chapter is on assembly, annotation, and the downstream comparative analysis functionality that is freely available in the resource. |
X Demographics
Geographical breakdown
Country | Count | As % |
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Unknown | 3 | 100% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 2 | 67% |
Scientists | 1 | 33% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 67 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 14 | 21% |
Student > Bachelor | 10 | 15% |
Student > Master | 7 | 10% |
Researcher | 6 | 9% |
Student > Doctoral Student | 5 | 7% |
Other | 9 | 13% |
Unknown | 16 | 24% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 18 | 27% |
Agricultural and Biological Sciences | 14 | 21% |
Immunology and Microbiology | 7 | 10% |
Computer Science | 4 | 6% |
Medicine and Dentistry | 2 | 3% |
Other | 7 | 10% |
Unknown | 15 | 22% |