TY - JOUR AU - Speiser, Daniel I. AU - Pankey, M. Sabrina AU - Zaharoff, Alexander K. AU - Battelle, Barbara A. AU - Bracken-Grissom, Heather D. AU - Breinholt, Jesse W. AU - Bybee, Seth M. AU - Cronin, Thomas W. AU - Garm, Anders AU - Lindgren, Annie R. AU - Patel, Nipam H. AU - Porter, Megan L. AU - Protas, Meredith E. AU - Rivera, Ajna S. AU - Serb, Jeanne M. AU - Zigler, Kirk S. AU - Crandall, Keith A. AU - Oakley, Todd H. PY - 2014 DA - 2014/11/19 TI - Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms JO - BMC Bioinformatics SP - 350 VL - 15 IS - 1 AB - Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. SN - 1471-2105 UR - https://doi.org/10.1186/s12859-014-0350-x DO - 10.1186/s12859-014-0350-x ID - Speiser2014 ER -