Example sentences for: pssm

How can you use “pssm” in a sentence? Here are some example sentences to help you improve your vocabulary:

  • The PSSMs were prepared by choosing one or more starting queries (seeds) for a set of most frequently encountered domains (see reference [ 28] for details) and run against the NR database until convergence with the -C option of PSI-BLAST to save the PSSM.

  • However, despite extensive comparisons using PSSM and careful visual examination, we failed to detect any residual sequence similarity between DDRP and RDRP, outside the core DPBB domain containing the metal-binding active site.

  • The non-redundant (NR) database of protein sequences (National Center for Biotechnology Information, NIH, Bethesda) was searched using the BLASTP program [ 100 ] . Position-specific scoring matrix (PSSM) searches were conducted using the PSI-BLAST program, typically with a PSSM inclusion expectation (E) value threshold of 0.01, and were iterated until convergence [ 100 101 ] . Prior to PSI-BLAST searches, query sequences were evaluated for compositional bias using the SEG program [ 102 ] . If no such bias was detected, searches were run with the composition-based statistics turned off, in order to maximize sensitivity [ 103 ] . Multiple alignments of protein sequence were constructed using the T_Coffee program [ 104 ] , followed by manual correction based on the PSI-BLAST results.

  • This PSSM was more conserved than the 25-mer PSSM described above, with bits for all positions ranging from 0.2 to 1.9 and an average bits/position of 0.9 (Figure 5).

  • We were able to align the canonical RSS nonamer and Sb with this PSSM.


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