PSI-BLAST uses multiple iterations to scan the database, with each iteration constructing a position-specific score matrix that replaces the simple query.
Moreover, after constructing a position-weight matrix and scanning the entire genome of P. acnes using PREDetector [ 77], we identified another pair of nrd-boxes far downstream of the nrdDG promoter active under the growth conditions used in this study.
The nodes organize into collaborative subtrees, then using simple geometric relationships each node constructs a position estimate and finally the estimate is refined using a least-squares method.
Briefly, we constructed a position weight matrix (PWM) for NRF2 (ARE motif) based on the collection of experimentally discovered AREs.
We have constructed a position weight matrix (PWM) based tool named sRNAscanner, using E. coli K-12 MG1655 sRNA-specific transcriptional signals as positive training data, for the identification of intergenic sRNAs.
For each of these subsets, we extracted all sequences of length 20 nt covering the region [−10,+10], and for each of the 16 such subsets we constructed a position weight matrix (PWM) following [36].
A common strategy for modeling the binding preferences of a transcriptions factor is to construct a position weight matrix (PWM) from known binding sites.
They constructed a position-specific scoring matrix (PSSM), and observed that the preferred residues for µ- calpain and m- calpain recognition are Leu, Thr and Val in the P2 position, and Lys, Tyr and Arg in the P1 position [16].
The second method entailed an initial iterated PSI-BLAST [ 34] search against the NCBI nonredundant protein database to construct a position-specific scoring matrix for each exon variant.
Probabilities for all possible substitutions at each position are then computed to construct a position-specific scoring matrix, where each entry in the matrix represents the probability p ca of observing amino acid a in column c in the alignment.
Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific score matrix (PSSM) for searching the database in round i + 1.
