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3PFDB database was designed to find a best representative sequence (BRS) for each PFAM family (6).
The study also indicates that a best representative sequence, which performs better with the PHI-BLAST than the MQ PSI-BLAST, can help save computational time and achieve better coverage.
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As the selection of a single, best representative PSSM from different members of the protein sequence families are currently performed in a non-standardized way, the data mining approach used in this work is a primary attempt in this regard.
The spatial offset was manually obtained by observing overlapping images of the two maps, while adjusting the offset to a value best representative of correct alignment that correlates with the video.
3PFDB is a collection of best representative PSSM profiles of 8,524 protein families from Pfam database.
We had earlier created 3PFDB database as a repository of best representative sequences, selected from each PFAM domain family on the basis of high coverage.
Availability of an approach to identify BRPs and a curated database of best representative PSI-BLAST derived PSSMs for 91.4% of current Pfam family will be a useful resource for the community to perform detailed and specific analysis using family-specific, best-representative PSSM profiles.
Conversely, a model organism might be desirable if it is the best representative for a specific mechanism despite being a very poor model for other phenomena or mechanisms.
For motifs in the two databases, we also performed an integration of the best representative from each cluster as done above.
"You get the best and brightest and do your level best," Representative Sherwood Boehlert, a New York Republican who is chairman of the House Science Committee, said in an interview.
Given the epidemiology of P. aeruginosa acquisition and the fact that our murine model was designed with the aim of recapitulating the pathogenesis of P. aeruginosa infection in a human host, we felt that using bacteria recovered from the drinking water was the best representative of a baseline condition.
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