Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The cu... A Bateman,E Birney,L Cerruti,... 被引量: 978发表: 2002年 The Classification of Protein Domains into Families and Clans through Entropy ...
Often, these models use Pfam domains, annotations assigned to protein sequences using a set of hidden Markov models (11), to inform the classification. The ability to computationally predict bacterial tolerance for stress from such genome annotations is currently limited to antibiotic resistance (15,...
In this chapter, the use of the web interface to Pfam and the resources provided (annotation, sequence alignments, phylogenetic trees, profile hidden Markov models [HMMs]) are described. The exploitation of tools for searching sequences against the library of Pfam HMMs, searching for domain ...
Data availability: ScienceOpen disciplines: Chemistry Keywords: Amino Acid Sequence, Databases, Factual, Models, Chemical, Molecular Sequence Data, Multigene Family, Plant Proteins, chemistry, Protein Structure, Tertiary, Seeds, Sequence Alignment, Sequence Homology, Amino Acid ...
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Pfam is a database of protein domain families, with each family represented by multiple sequence alignments and profile hidden Markov models (HMMs). In add... P Coggill,RD Finn,A Bateman - Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 被引量: ...
We find that, rather irrespectively of the global superimposition of the pairwise models, Pfam-containing regions overlap with a TM-score above 0.8 and a predicted local distance difference test (pLDDT) which is higher than the rest of the modeled sequence. This indicates that both methods are...
Analyses based on gene tree, genome synteny, and structural models revealed rapid adaptive evolution of this array through gene duplication, gene loss, and functional diversification. Individual PFam54 genes, however, do not show high intra-population sequence polymorphisms as genes providing evasion ...