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Example sentences for: pssms

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Representative results of passes of MEME with W = 9 nucleotides are presented in Figures 5, 6, 7, 8, 9. In those passes, two PSSMs were discovered in the ZAS-N dataset.
In addition, the information content (measured in bits), which reflects the degree of conservation of each column (or position) in those PSSMs was relatively low, ranging from 0 to 1.7, with an overall average <0.
After cloning and DNA sequencing, the KRC-selected sequence datasets were analyzed by the computer program Multiple Expectation Maximum for Motif Elicitation (MEME version 3.0) to generate sets of position specific scoring matrices (PSSMs) or motifs [ 30 ] . When the program was set to identify wider sequences (= 9 nucleotides) the PSSMs were homologous to Sb [ 29 ] , the κB motif [ 31 ] , and the canonical heptamer and nonamer elements of the RSS [ 32 ] . However, shortening the width of the motifs to 5 nucleotides, the target length for the C 2 H 2 zinc finger pairs of the tramtrack [ 33 ] , the ZAS-N dataset yielded two motifs, "GGTAT" and "T(T/C)TT(T/G)G" and the ZAS-C dataset yielded a single motif, "TGTGG".
All globular segments of proteins that did not map to domains with previously constructed PSSMs were searched individually using PSI-BLAST to detect any additional domains that may have been overlooked.
The 3D-Genomics database [ 12 ] uses SCOP domain PSSMs from 3D-PSSM [ 13 ] . Gene3D uses the CATH domain classification to annotate genes and genomes [ 14 ] .