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Showing 1 to 6 of 6 for “"remote homology"”.
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Exploiting gene expression and protein data for predicting remote homology and tissue specificity
… gene expression and functional annotations: (a) remote homology detection based on amino acid sequences and secondary structures; (b) the analysis of tissue-specific gene expression for predictive signals in the sequence and secondary structure of the resulting protein product; and (c) a study of …
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Structural RNA Homology Search and Alignment Using Covariance Models
… CMs) are powerful computational tools for homology search and alignment that score both the conserved sequence and secondary structure of an RNA family. However, due to the high computational complexity of their search and alignment algorithms, searches against large databases and alignment …
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Characterization of Mitochondrially Targeted T3SS2 Effectors in Vibrio parahaemolyticus
… kinases. Coupling structural modeling and remote homology prediction with biochemistry, we determined that residue D205 in VPA1328 was critical for its catalytic activity. Using cell biology, we found VPA1328 localizes to the mitochondrial matrix of eukaryotic cells. Interestingly, while …
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Statistical estimation problems in phylogenomics and applications in microbial ecology
… of profile hidden Markov models that improves remote homology detection. The second is a data visualization technique that generates an image of the community with a high density of data, but one that makes it naturally easy to compare many different samples at a time, potentially uncovering …
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Using structure to explore the sequence alignment space of remote homologs
The success of protein structure modeling by homology requires an accurate sequence alignment between the query sequence and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence …
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A thermodynamic definition of protein folds
Modern techniques in structural biology, like homology modeling, protein threading, protein fold classification, and homology detection have proven extremely useful. For example, they have provided us with evolutionary information about protein homology which has in some many cases lead directly to …