Doug Hyatt

TL;DR: This work developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm), which achieved good results compared to existing methods, and it is believed it will be a valuable asset to automated microbial annotation pipelines.

TL;DR: MetaProdigal is presented, a metagenomic version of the gene prediction program Prodigal that can identify genes in short, anonymous coding sequences with a high degree of accuracy and can identify sequences that use alternate genetic codes and confidence values for each gene call.

TL;DR: This article reconstructed composite, near-complete approximately 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate.

TL;DR: In this paper, a stable isotope probing (SIP) method was used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample.

TL;DR: The score can be used to set thresholds for screening data when analyzing “all published genomes” and reference data is either not available or not applicable and the scores highlighted organisms for which commonly used tools do not perform well.