This tool is designed for the preliminary diagnosis of the query sequence.
What is Phylogenetic Marker? Phylogenetic marker is a fragment (locus) of either coding or non-coding DNA which is used for phylogenetic reconstructions.
For example, the sequence of tef1 gene which is encoding the EF-1alpha protein, contains three phylogenetic markers such as 4th and 5th introns (large and short, respectively) and 6th exon. At the same time there is no full agreement between researchers concerning to which primers pairs (= which fragments of the gene) should be sequenced. Therefore it is often that sequences that deposited in GenBank are significantly larger or shorter than any of these phylogenetic markers. As a consequence the NCBI BLAST may provide an unclear result.
In order to increase the accuracy of the identification based on the similarity search (BLAST) we have created (i) a vouchered Multiloci Database of Phylogenetic Markers and (ii) TrichoMARK v. 1.0 - a program which will first detect phylogenetic markers from the query sequence and then retrieve them for the following similarity search against the vouchered Multiloci Database of Phylogenetic Markers.
We suggest that this feature will significantly increase the accuracy of the obtained results!
Read more: Kopchinskiy et al., 2005