Words similar to phi-blast

Example sentences for: phi-blast

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Multiple alignment constructed on the basis of sequence alignments produced in the PSI-BLAST and PHI-BLAST searches and superposition of the predicted secondary structure elements of RDRP and the experimentally determined structure of DDRP revealed considerable concordance between the RDRP and DDRP families.
We also ran database searches using the PHI-BLAST program that combines a regular BLAST search with a pattern search [ 60 ] . In these searches, the active site motif was used as the pattern query, and various RDRP sequences as the sequence queries.
Identification and statistical evaluation of conserved motifs in multiple protein sequences were performed using the Gibbs sampling method as implemented in the MACAW program [ 105 106 ] . Pattern searches were conducted using the GREF program of the SEALS package [ 107 ] , and pattern-initiated BLAST searches were carried out using the PHI-BLAST program [ 60 ] ?. Protein structure databases were searched for similar structures using the DALI program [ 108 ] . Protein secondary structure was predicted using the PHD program implemented on the PredictProtein server with a multiple alignment submitted as the [ 109 110 ] . Protein structures were visualized and manipulated using the Swiss-PDB viewer program [ 111 ] and the ribbon diagrams were made using MOLSCRIPT [ 112 ] .