Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 24 for “"Multiple sequence alignments"”.
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Modeling Evolutionary Constraints and Improving Multiple Sequence Alignments using Residue Couplings
… Most of these methods primarily use a multiple protein sequence alignment---most likely a resultant alignment---which better exposes couplings and is obtained through manual tweaking of an alignment constructed by a classical alignment algorithm. Classical alignment algorithms primarily …
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ChaperoNet: Distillation of Language Model Semantics to Folded Three-Dimensional Protein Structures
… to capture the evolutionary semantics of protein sequences, and as an emergent property, were found to be structural learn- ers. Enriched with multiple sequence alignments (MSA), these transformer models were able to capture significant information about a protein’s tertiary structure. In this …
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Detection of non-coding RNA with comparative genomics and the sequential closure of smooth graphs in Cartesian currents
… significant base pairs in ncRNA genes in multiple sequence alignments of cross-species homologs, a divide-and-conquer approach to optimal assembly of exon predictions with O(n log n) time-complexity, (the standard algorithm for exon assembly has O(n²) time-complexity for ncRNA exon …
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Constructing Phylogenetic Networks based on Trinets
… level-1 phylogenetic networks directly from multiple sequence alignments.
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Genome wide search for pseudo knotted non-coding RNAs
… to scan through the genome and align its sequence segments to some structure model for the ncRNA family. With the recent advances in detecting an ncRNA in the genome, heuristic techniques are designed to perform an accurate search and sequence-structure alignment. This study uses a novel …
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Phylogeny of the Resistance-Nodulation-Cell Division (RND) Superfamily
… Exhaustive searches of selected representative sequences through BLAST (Mistry et al. 2013) and HMMSearch (Camacho et al. 2009) created the most comprehensive and up-to-date dataset to establish all possible RND homologs. CD-HIT, a clustering software, was used to refine our dataset (Pearson …
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In silico prediction of non-coding RNAs using supervised learning and feature ranking methods
… on features derived from folding the consensus sequence of multiple sequence alignments using different folding programs: RNAalifold, CentroidFold, and RSpredict. The method ranks these folding features according to a Class Separation Measure (CSM) that quantifies the ability of the features to …
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Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework
… highly conserved sites, and rely heavily upon multiple sequence alignments. However, sequence conservation based approaches have limited ability to detect lineage-specific elements that could contribute to species-specific traits. In this thesis, we describe a novel framework that utilizes a …
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Efficient algorithm for selecting protein residue-residue contacts
… allows us to predict the contacts from multiple sequence alignments. The predicted contacts can then be used as spatial constraints and offer guidance in protein structure prediction. The constraints can be used as inputs to a protein structure prediction algorithm to produce ""decoy"" …
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Algorithmic Developments for Sequence Analysis, Structure Modeling and Functional Prediction of Proteins
Sequence, structure and function, being the three most important properties of proteins, are interrelated through homology relationships. In this post-genome era, we are equipped with abundant sequence information. Homology inference is thus of great practical importance because of its ability to …
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Progress Towards Integrated Models of HCV Dynamics
… approach, in which we analyzed HCV multiple sequence alignments (MSAs) to identify covariant amino acid positions within HCV proteins. Some of the challenges to the study of covariation in HCV MSAs were identified, and we describe a novel method of calculating covariation which …
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Structural and Computational Studies of RNA Polymerase
… conserved DNA bases. (2) Created comprehensive multiple sequence alignments for the two bacterial large subunits (β/β′) and their homologues from the following multisubunit RNAPs: bacterial, eukaryotic pol I/II/III, Nuclear-Cytoplasmic Large double-stranded DNA Viruses, archeal, and plant …
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Molecular assembly and function of Androglobin, a novel chimeric globin.
… by recombinant techniques. Comparing 362 Adgb sequences using multiple sequence alignments, the critical amino acids of the haem domain were identified as the proximal His F8, distal Gln E7, and CD1 Tyr residues. Consistent with the literature, Adgb does not have a close phylogenetic …
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A phylogenetic study of ubiquitin conjugating enzymes and structural analysis of human UBE2J proteins
… organisms whose genomes have been fully sequenced, and also the review of the nomenclature of yeast and human UBCs. The main findings were:<br/><br/>1) The successful construction of Phylogenetic trees containing all 14 yeast UBCs and UBC-like proteins and their homologues in selected …
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Exploring the evolution of social behaviour using genomic data
… technology to generate the brain Expressed Sequence Tags (ESTs) of twelve socially diverse bees. The ESTs were assembled into species-specific non-redundant contigs and singletons, which were loaded into a MySQL database using custom scripts. The Honey Bee Homolog Blast website was designed …
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Algorithm development for RNA structure prediction in RNA viruses
… theoretically form can be problematic. Since the sequences of RNA viruses evolve rapidly and, for many species, there are a large number of sequenced isolates, comparative genomics can be used to predict structures that are conserved and therefore more likely to be biologically relevant. Here, a …
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Biochemische, molekularbiologische und genetische Untersuchungen über strukturelle Voraussetzungen für DNA U-Endonukleaseaktivität in der ExoIII-Familie von DNA Reparaturenzymen
… aber gegenüber U/G. Aufgrund der Analyse eines multiple sequence alignments von Mth212 mit der ExoIII-Familie und der 3D Struktur bereits kristallisierter ExoIII-Enzyme wurden bei M. mazei ExoIII zwei Aminosäuren ausgetauscht, was zur generellen Steigerung aller Aktivitäten und damit zu einer …
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Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes
Large single-stranded nucleotide sequences such as certain DNA and RNA virus genomes form complex secondary structures through Watson-Crick base-pairing interactions between bases on the same DNA or RNA strand. Both computational and experimental methods are available for determining the secondary …
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Algorithms for estimating rates of nucleotide change
… substitution rates between species from multiple sequence alignments. To address the problem of estimating mutation rates within species, Vogl (2014) has developed a general algorithm for the case of bi-allelic neutral evolution. A necessary first step in generalizing the Vogl estimator …
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