Databases
The Barcoding Tool2 for Bromeliaceae uses 3 BLAST databases.
- agtI (agtI Exon+Intron) – 561 Sequences (315875 bp)
- agtIex (agtI exon only) – 442 Sequences (154543 bp)
- matK – 233 Sequences (195191 bp)
Databases where created using (and will be queried with) BLAST version 2.2.31+.
Usage
Submit marker sequence(s) matching one or more of those databases in FASTA format and press "Submit". Use sequences from one individual, optionally up to 3 markers.
Output
You will get the top scoring database sequences (if available) for each of the databases in the form of a standard BLAST result. Hover your mouse pointer over the summary table to see some basic explanations. If available there's the possibility to view a reference image for matching species. Below the summary table the best results are plotted into a phylogenetic diagram of the family, color-coded according to the respective database.
Interpretation
The BLAST hits are by no means equivalent to a careful determination by an expert. It is up to the user to assess plausibility of the results obtained by this tool. E-values for top hits should be near zero and Bit-scores reasonably high with a query coverage near the full length of the sequence. It is not a given that the hit sorted highest in the list corresponds to your sample species. If hits are very similar, sorting tends to be inaccurate. Also, the database is not exhaustive, not every species is included, so best hits are probably "only" closely related to your query, not necessarily identical. The barcoding tool is intended to provide a hint of where a given individual is probably to be placed in the Bromeliaceae phylogeny. If the different databases provide incongruent results the "determination" is to be considered unreliable.
