Keeley Collins
Faculty Advisor: Zhangjun Fei
Year: 2018
Mentor: Yi Zheng

“SpinachBase: A new database for spinach research and development”

 

Project Summary:

SpinachBase (www.spinachbasez.feilab.net) is a new web-based database for the Spinacia oleracea genome providing centralized public access to genomic and transcriptomic data as well as analytical tools to assist further research in spinach. Through the database, the whole genome sequence for spinach is available to browse or download with a variety of annotations. Those annotations include genes, mRNA, and other features; gene homologs; association of InterPro protein domains; Gene Ontology (GO) terms; and genome pathway terms. The annotations are available in genome (feature) pages, and may also be queried using a search interface and viewed in JBrowse, a genome browser.  Transcriptome (RNA-Seq) data for 120 different accessions of spinach (wild and cultivated) may also be viewed in JBrowse (a genome viewer). Metabolic pathway information is available through the SpinachCyc database. SpinachBase also provides tools for analysis like NCBI BLAST, GO Enrichment analysis, Pathway Enrichment analysis, and batch downloads of specific sequences and annotations.

My Experience:

I’ve done bioinformatics research in the past at my university, however working at BTI was the first time that I’ve worked in a large lab. I really enjoyed spending time with them. Many people in my lab were post docs or graduate students so I gained a lot by talking with them about their experiences and research. In my research I encountered a large variety of different problems to solve, and had to work with a few different programming languages that I hadn’t worked with previously. Due to these challenges, my troubleshooting and programming skills have really increased. Being an intern at BTI is nice because if you run into problems or get stuck with research your mentor and lab can help you, and since you are with a group of other interns you can all swap stories and experiences and really support each other.