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These runtime requirements are likely to become even more severe due to the rapid growth in size of both sequence and model databases.
This conversion procedure effectively prepares the HMMer-style HMM for "FS" style search (local in both sequence and model, with the possibility of finding multiple instances of the model in the sequence).
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Classifications using both sequence and structure used a mixture model with both the discrete and continuous distributions.
Decoding: Given an observation sequence and model parameters, determine the corresponding optimal state sequence.
The methodology implied by eq. 2 and 3 can also be applied to the mixture model including both sequence and structure information.
In this paper we present a novel method base on SVM model integrating both sequence and structural information to predict protein-ligand binding site.
Interestingly, both coding sequence and promoter models yielded sequence words that could be used to predict the MSL-binding status of genes excluded from the modeling.
The method uses SNPs and alternative mRNA isoforms mapped to EST sequences and models both regulated alternative splicing as well as allele-specific splicing.
Both sequence comparison and homology modeling indicated that Asp and Glu residues were the catalytic nucleophile and proton donor, respectively [ 11].
The sequence alignment and model have several convincing features.
Taxon sampling, sequence length and model selection for data partitions.
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