Correction: Double triage to identify poorly annotated genes in maize: The missing link in community curation.

[This corrects the article DOI: 10.1371/journal.pone.

Analysis of DNA Barcodes Using DNA Subway.

DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads.

A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding.

This rapid, equipment-free DNA isolation procedure using chromatography paper is a simple method that can be performed in less than 30 min and requires no wet lab experience. With minimal expense, it offers an affordable alternative for anyone wanting to explore biodiversity. It also provides an excellent option for use in classrooms or other activities that are time limited.

Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification.

Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud.

MaizeCODE is a project aimed at identifying and analyzing functional elements in the maize genome. In its initial phase, MaizeCODE assayed up to five tissues from four maize strains (B73, NC350, W22, TIL11) by RNA-Seq, Chip-Seq, RAMPAGE, and small RNA sequencing. To facilitate reproducible science and provide both human and machine access to the MaizeCODE data, we enhanced SciApps, a cloud-based portal, for analysis and distribution of both raw data and analysis results.

Double triage to identify poorly annotated genes in maize: The missing link in community curation.

The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer.

DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists.

DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity.

An innovative plant genomics and gene annotation program for high school, community college, and university faculty.

Today's biology educators face the challenge of training their students in modern molecular biology techniques including genomics and bioinformatics. The Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory has developed and disseminated a bench- and computer-based plant genomics curriculum for biology faculty. In 2007, a five-day "Plant Genomics and Gene Annotation" workshop was held at Florida A&M University in Tallahassee, FL, to enhance participants' knowledge and understanding of plant molecular genetics and assist them in developing and honing their laboratory and computer skills.