Finally, the redundant sequences were collapsed using the CD-HIT-EST algorithm [ 105], producing a total of 98,515 sequences.
Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*).
However, in 1994, when a microbial genome-sequencing project was contemplated at TIGR, a whole-genome shotgun sequencing approach was considered possible with the TIGR EST assembly algorithm.
In order to retain alternative splicing information, Heber et al [ 14] developed an EST assembly algorithm that retains all the junctions in the de Bruijn graph.
Employing the new EST assignment algorithm and the novel statistical method, a similar subtractive screen to Huminiecki and Bicknell 2000 [ 8] was carried out but this time with the most recent publicly available data.
A similar approach is employed in Prot4EST [ 14] which links together several EST prediction algorithms.
Most prominently, a succession of single-linkage EST clustering algorithms which use the d distance metric (Hide et al., 1994) [see d2_cluster (Burke et al., 1999); CLU (Ptitsyn and Hide, 2005); and more recently, wcd (Hazelhurst et al., 2008)].
The program Ensembl, which continuously scans the nearly completed human genome sequences obtained as part of the Human Genome Project and combines information from EST databases and prediction algorithms, has already identified more than 35,000 putative genes.
In the present work, the screening of the P. glauca EST database using the TBLASTN algorithm resulted in identification of five new defensin-encoding genes.
The CD-hit-EST V4.5.4 clustering algorithm [ 78, 79] was used to reduce redundancy within this long-read pre-assembly (sequence identity threshold 0.95; word length 8).
In search of (novel) members of the pacifastin family in the available genome and EST databases, BLASTN and TBLASTN algorithms were performed, using a list of 16 known pacifastin-related precursor sequences from the Uniprot protein database as a query [ 9].
