Multiple sequence alignments and conserved amino acids
Data mining for important amino acid residues in multiple sequence alignments and protein structures
... a multiple sequence alignment and a 3D structure of one protein in PDB ...seven sequence- based and two structure-based features, each of which was shown to contribute to classification ...the ...
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AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences
... assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most ...restrictive. Conserved/divergent regions ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... as sequence retrieval, computation of alignments and commu- nication with ...of conserved and variable positions in the alignment, reordering and deletion of sequence by drag-and-drop, and ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... as sequence retrieval, computation of alignments and communication with ...of conserved and variable positions in the alignment, reordering and deletion of sequence by drag-and-drop, and ...
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Noisy: Identification of problematic columns in multiple sequence alignments
... Such alignments can be improved by increasing the sig- nal-to-noise ratio through exclusion of noisy ...of conserved blocks, known to improve phylogenetic analysis and car- ried out manually, are common ...
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OD-seq: outlier detection in multiple sequence alignments
... ing sequence outliers have mainly concentrated on finding sections of sequence or alignment which are highly diver- ...of amino acids with suspiciously low simi- larity scores to the ...
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Noisy: Identification of problematic columns in multiple sequence alignments
... by sequence constraints due to environmental pres- sure can produce a considerable amount of phylo- genetic noise in the data and so-called “bad” and phylogenetically misleading ...of conserved blocks, ...
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IVisTMSA: INTERACTIVE VISUAL TOOLS FOR MULTIPLE SEQUENCE ALIGNMENTS
... test alignments against a single reference ...test alignments are displayed in tabular ...test alignments in form of bar, pie and line ...test alignments have conserved ...reconstruct ...
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Mutational Analysis of Conserved Amino Acids in the Influenza A Virus Nucleoprotein
... Incorporation efficiency of multiple vRNA segments into VLPs containing mutant NPs. As described above, we found that R74A, R156A, R175A, R195A, R199A, and R361A sup- port VLP incorporation of a single vRNA ...
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RNAstrand: reading direction of structured RNAs in multiple sequence alignments
... any multiple sequence alignment based on well-established energy parameters and dynamic programming algo- ...size, sequence and GU base pair variation in the input alignment, these features are ...
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Multiple sequence alignments of partially coding nucleic acid sequences
... well-conserved amino acid sequence but ex- hibits high variability at the nucleic acid ...non-coding sequence in the intron and the flanking sequences are highly ...as amino ...
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DendroBlast: approximate phylogenetic trees in the absence of multiple sequence alignments
... protein sequence alignments from a previous analysis comprising 308 simulated multiple sequence alignments ...These alignments were simulated on realistic tree topologies ...
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EvalMSA: a Program to Evaluate Multiple Sequence Alignments and Detect Outliers
... More recently, a different approach has been taken. Some- times, a divergent sequence is included in a group of conserved or close (in evolutionary terms) sequences. This inclusion can alter the whole ...
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Detecting species-site dependencies in large multiple sequence alignments
... Neither sequence-based nor site-based methods are on their own able to detect any recombination ...30 amino acid transfer region in the beginning of the ...like sequence logos or clustering ...
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In Vivo Incorporation of Multiple Unnatural Amino Acids
... predominately translated in vivo. Another advantage for the oocyte system is that the most used Arg triplets (AGG and AGA) (27) would not be recognized by the modified FS tRNAs used in this study. Therefore all possible ...
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Contribution of conserved amino acids in mediating the interaction between EBNA2 and CBF1/RBPJk.
... of amino acid sequence conservation (23% identity) between HVP EBNA2 and the human proteins outside these three conserved regions ...positionally conserved hydrophobic residues between aa 252 ...
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Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
... Furthermore, there is a limitation of the presented method with regard to interaction sites that are located outside conserved RNA structures. These regions are hard to align if they are, in addition, sequentially ...
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Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs
... larger alignments, we selected one of the largest alignments from the OXBench suite [119], consisting of 122 immunoglobulin sequences, with average length ...as amino acid content and sequence ...
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ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments
... same sequence remain connected in the visualization, multi-site sequence motifs become visible even between distant ...motifs conserved through functional similarity, not ...
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3D representations of amino acids—applications to protein sequence comparison and classification
... where N mat is the number of positions in the correspondence. The cRMS however is not a good measure of structural similarity [54,60]. Intuitive- ly, a measure based on the geometric properties of an alignment should ...
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