Words similar to pssm
Example sentences for: pssm
How can you use “pssm” in a sentence? Here are some example sentences to help you improve your vocabulary:
E -values less than 7. Thus, the PSSM was very effective at discriminating between GshA and non-GshA sequences in the database.
MatDB, based on PEDANT analysis of Arabidopsis thaliana , provides structural annotations using SCOP domain position specific scoring matrix (PSSM) profiles.
MEME analyzes input sequences for similarities and produces a PSSM or motif for each pattern it discovers [ 30 ] . We set the parameters of MEME as follows: (i) zero or one occurrences of a single motif per sequence; (ii) five as the maximum number of motifs to identify; (iii) 5 to 25 nucleotides as the range of motif size; and (iv) both DNA strands as input.
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.
A search of the non-redundant database using a PSSM (position-specific scoring matrix) generated from these blocks retrieved a total of 81 sequences with E -values less than 10.
Loading...