POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

Abstract

The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time-sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn's utility are provided herein.

Figure 1

Sequence-indexed data search: sequence to stocks and publications. To locate stocks with mutations in or near the sequence of interest as well as relevant publications simultaneously, the process consists of steps demarcated by red circles. (a): (1) Paste a sequence (FASTA-formatted or raw) or sequence identifier (GenBank accession number or GI) into the “Input sequence” field and indicate whether the sequence is made up of nucleotides or amino acids. (2) Next, select one or more datasets to search. Here, mutant seed stocks and publications are selected. (3) Type an email address into the text box (optional) then click the “Begin search” button. (b): (4) The number of results from each search type are shown. Once a results set has been chosen (here “UniformMu”), (5) BLAST parameters used to produce the results are displayed. (6) The algorithm for conducting the selected search is shown, and (7) identified gene models and stocks are listed along with a snapshot of the MaizeGDB Genome Browser in the region of the mutation to show genomic context. (c): (8) The number of results from each search type is shown. Once a results set has been chosen (here “publications”), (9) BLAST parameters used to produce the results are displayed. (10) The algorithm for conducting the selected search is shown, and (11) identified citations are shown with links to both PubMed and MaizeGDB.