The fact that the PSSMs obtained iteratively from nr based on SUPERFAMILY consensus seeds generally perform better than those originating from Pfam consensus seeds shows the importance of the choice of the initial seed sequence.
We call the resulting consensus maps seed maps.
In total, 70 consensus motif seeds were generated from the set of 18 MafB binding genes by motif extraction, and were given individual ID numbers.
This is further emphasized by the slightly better performance of the PSSMs based on the consensus sequence as seed (PCU) than the performance of those based on the seeds taken from ASTRAL (PSU).
Similarly, the Smith-Waterman algorithm is applied to the seed consensus and all non-seed supergenes to get non-seed cores.
A seed consensus sequence is formed from these cores by finding the nearest frequency profile cluster in each position of this seed pairwise alignment.
The latter helps define the subgroup inasmuch as the corresponding pattern is required to match the consensus for the seed alignment.
In total, 103 vs 43 QTLs and 24 vs 2 digenic epistatic interactions were identified on the consensus map for seed and skin PA variables, respectively.
Li et al. [ 23] identified 13 consensus QTL for seed weight and 9 QTL for silique length; these QTL explained 0.7 67.1 % and 2.1 54.4%% of the phenotypic variance in seed weight and silique length in rapeseed, respectively.
The Table 4 lists the number of novel pre-miRNAs predicted for each sample; and the details of the predicted novel pre-miRNAs including the information regarding the miRdeep score, mature miRNA read count, miRNAs with same seed region, consensus mature miRNA sequence, consensus precursor miRNA sequence, precursor miRNA genomic coordinates, for each tissue sample is given in Additional file 6.
8 With respect to stranded versus loose seeds, the consensus panel felt there may be a reduced potential for seed migration with stranded seeds, particularly at the periphery.
