Sequences analysis and alignments
Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
... aligning sequences on downstream analyses, previous studies employed se- quence length cutoffs that have been gauged by a variety of ...sequence alignments, while bimodality was not observed at shorter ...
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Multiple sequence alignments of partially coding nucleic acid sequences
... sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence ...acid sequences, however, exhibit a much larger sequence ...
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Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences
... antibody sequences from mice and humans, we infer an empirical amino acid substitution model AB, which is specific to antibody ...antibody sequences, as demonstrated on large next generation sequencing ...
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AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences
... Analysis of gene and genomic variation has been revo- lutionised by the advent of next-generation sequencing technology, revealing a considerable degree of genomic polymorphism. This has led to studies focusing on ...
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SeqTools: visual tools for manual analysis of sequence alignments
... match sequences aligned against the genomic reference ...sequence alignments and to perform a combination of manual and automatic processing of the ...reference alignments are essential if they are ...
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Analysis of Chimpanzee History Based on Genome Sequence Alignments
... sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a ...macaque. Analysis provides a more precise ...
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MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences
... multiple alignments, we made several pruned versions of the multiple alignments by selecting different subsets of the available species, ranging from only the melanogaster sequence, to sequences from ...
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Spectral Analysis of Protein Sequences
... Variability Profiles in Entropy and Factor Scores To accurately and robustly define the variability of alphabetic data, we apply tools from information theory. Specifically, we use entropy profiles to measure the residue ...
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Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments
... Findings: The genetic variation found in six M. tuberculosis strains does not involve significant genomic rearrangements. Most of the variation results from deletion and transposition events preferentially associated ...
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Phylogenetic Analysis of Polyomavirus BK Sequences
... sequence alignments based on limited data derived from the VP1 ...This analysis supports the classification of BKV into six genotypes, of which types V and VI have not been previously ...
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A basic analysis toolkit for biological sequences
... sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost ...
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Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family
... between sequences is not measured by summing up, over all sites, properly specified individual similarity scores, but rather by comparing whole sequence segments of equal length with each ...other. ...
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Incorporating regional context into pairwise alignments of biological sequences
... truncated alignments under search keys prefixed by BBS in order to construct PIPs. This approach avoids effects due to large end gaps and increases the chance of the optimiser finding global optima, rather than ...
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Alignments of DNA and protein sequences containing frameshift errors
... The alignments of the translation of the rat mRNA and cercarial elastase using the Smith-Waterman algorithm before and after three deletion errors were introduced, where the rat mRNA is [r] ...
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Detection of Distinct URL and Removing DUST Using Multiple Alignments of Sequences
... © 2016, IRJET | Impact Factor value: 4.45 | ISO 9001:2008 Certified Journal | Page 928 cluster. Then rules are generated from these sequences. For large clusters, which are rare, we adopt a heuristic similar to ...
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Antibody-specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences
... Moreover, additional diversity is introduced later on by a further maturation process, known as somatic hypermutation, which comprises the mutation of nucleotides in the newly created VH and VL region gene segments. This ...
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KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences
... of sequences that are highly similar, although it does function with different genotypes of a virus species such as dengue ...format sequences that have 1) minor differences in length and 2) very few indels ...
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Region Alignments for Reclassification
... ( ) Schools that opted to move down in classification to replace a team that moved up.[r] ...
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MUTATIONS AND SEQUENCE ALIGNMENTS
... sequence alignments contained in T (! [8] , [1010]), T (! [8] , [0110]) and T (! [8] , [1100]) that encode multiple sequence alignments between the sequences of Anne, Bob and ...
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FINAL REGION ALIGNMENTS
... Oglethorpe Murray County North Murray Ringgold Sonoraville REGION 7 Banks County Dawson County East Hall Fannin County Franklin County Lumpkin County West Hall REGION 8 Ea[r] ...
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