title: 'PACLIMS': a component LIM system for high-throughput functional genomic analysis.
abstract: BACKGROUND
  Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the approximately 11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required.
  
  
  RESULTS
  The platform designed, named PACLIMS, was built to support our high throughput pipeline for generating 50,000 random insertion mutants of Magnaporthe grisea. To be a useful tool for materials and data tracking and storage, PACLIMS was designed to be simple to use, modifiable to accommodate refinement of research protocols, and cost-efficient. Data entry into PACLIMS was simplified through the use of barcodes and scanners, thus reducing the potential human error, time constraints, and labor. This platform was designed in concert with our experimental protocol so that it leads the researchers through each step of the process from mutant generation through phenotypic assays, thus ensuring that every mutant produced is handled in an identical manner and all necessary data is captured.
  
  
  CONCLUSIONS
  Many sequenced eukaryotes have reached the point where computational analyses are no longer sufficient and require biological support for their predicted genes. Consequently, there is an increasing need for platforms that support high throughput genome-wide mutational analyses. While PACLIMS was designed specifically for this project, the source and ideas present in its implementation can be used as a model for other high throughput mutational endeavors.
authors.affiliation: Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC, USA. ndonofr@unity.ncsu.edu
authors.forename: Nicole
authors.initials: N
authors.lastname: Donofrio
authors.forename: Ravi
authors.initials: R
authors.lastname: Rajagopalon
authors.forename: Douglas
authors.initials: D
authors.lastname: Brown
authors.forename: Stephen
authors.initials: S
authors.lastname: Diener
authors.forename: Donald
authors.initials: D
authors.lastname: Windham
authors.forename: Shelly
authors.initials: S
authors.lastname: Nolin
authors.forename: Anna
authors.initials: A
authors.lastname: Floyd
authors.forename: Thomas
authors.initials: T
authors.lastname: Mitchell
authors.forename: Natalia
authors.initials: N
authors.lastname: Galadima
authors.forename: Sara
authors.initials: S
authors.lastname: Tucker
authors.forename: Marc J
authors.initials: MJ
authors.lastname: Orbach
authors.forename: Gayatri
authors.initials: G
authors.lastname: Patel
authors.forename: Mark
authors.initials: M
authors.lastname: Farman
authors.forename: Vishal
authors.initials: V
authors.lastname: Pampanwar
authors.forename: Cari
authors.initials: C
authors.lastname: Soderlund
authors.forename: Yong-Hwan
authors.initials: YH
authors.lastname: Lee
authors.forename: Ralph A
authors.initials: RA
authors.lastname: Dean
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods*; D004247:DNA / Q000378:metabolism; D004252:DNA Mutational Analysis; D003627:Data Interpretation, Statistical; D003628:Database Management Systems; D016208:Databases, Factual; D030541:Databases, Genetic; D019143:Evolution, Molecular; D015723:Gene Library; D005800:Genes, Fungal; D016678:Genome; D016681:Genome, Fungal; D020407:Internet; D020082:Magnaporthe / Q000235:genetics*; D009154:Mutation; D016366:Open Reading Frames; D020543:Proteome; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome; D004247:DNA