Name
Title | ||
|---|---|---|
Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. |
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2014 | 10.1186/s12859-014-0350-x | BMC Bioinformatics |
Keywords | Field | DocType |
bioinformatics,vision,phototransduction,galaxy,microarrays,biomedical research,evolution,transcriptomes,algorithms | Genome,Phylogenetic tree,Gene,Biology,DNA sequencing,Bioinformatics,Genetics,Phylogenetics,Gene family,Sequence assembly,DNA microarray | Journal |
Volume | Issue | ISSN |
15 | 1 | 1471-2105 |
Citations | PageRank | References |
4 | 0.34 | 13 |
Authors | ||
18 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Daniel I. Speiser | 1 | 4 | 0.34 |
| M. Sabrina Pankey | 2 | 11 | 0.76 |
| Alexander K. Zaharoff | 3 | 4 | 0.34 |
| Barbara A. Battelle | 4 | 4 | 0.34 |
| Heather D. Bracken-Grissom | 5 | 4 | 0.34 |
| Jesse W. Breinholt | 6 | 4 | 0.34 |
| Seth M. Bybee | 7 | 4 | 1.69 |
| Thomas W. Cronin | 8 | 5 | 0.72 |
| Anders Garm | 9 | 4 | 0.34 |
| Annie R. Lindgren | 10 | 4 | 0.34 |
| Nipam H. Patel | 11 | 4 | 0.34 |
| Megan L. Porter | 12 | 5 | 0.72 |
| Meredith E. Protas | 13 | 4 | 0.34 |
| Ajna S. Rivera | 14 | 4 | 0.34 |
| Jeanne M Serb | 15 | 7 | 0.68 |
| Kirk S. Zigler | 16 | 4 | 0.34 |
| Keith Crandall | 17 | 97 | 14.34 |
| Todd H Oakley | 18 | 14 | 1.20 |