Sequencing, sequence alignments and cluster analysis
Large-Scale Pairwise Sequence Alignments on a Large-Scale GPU Cluster
... parallel sequencing techniques to generate a large set of short DNA ...of analysis methods relies on clustering the DNA frag- ments based on a similarity ...ual alignments are relatively inexpensive, ...
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Analysis of Chimpanzee History Based on Genome Sequence Alignments
... Genetic Measurements Are Consistent between Our Data and Previous Studies Traditional population genetic data sets are based on small numbers of loci that are amplified by PCR and studied in multiple samples from each ...
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Cluster Analysis Method for Multiple Sequence Alignment
... high-quality sequence alignments, and occasionally in adjusting the final results to reflect patterns that are difficult to represent algorithmically (especially in the case of nucleotide ...to ...
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SNP-E: A New Method For Multiple Sequence Alignments Analysis And Accurate Single Nucleotide Polymorphism Evaluation
... multiple sequence alignments (MSA) involves looking across MSA and identifying base discrepancies (Wegrzyn et ...generation sequencing data (DePristo et ...depth sequencing to perform ...
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SeqTools: visual tools for manual analysis of sequence alignments
... missing/misaligned sequence and to identify splice sites and polyA sites and ...identify sequence that is not represented (or is misrepresented) and to quickly compare annotated gene models with ...
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ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments
... two alignments, aggregative motif visualization methods fail to capture the sequence ...Therefore, sequence logos are in general not able to help in the identification of specificity determining ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... (JavaScript Sequence Alignment Viewer) is a novel JavaScript component that adds to this ...further analysis, and highlight regions of the align- ment corresponding to the CDR loop regions of antibod- ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... multiple sequence alignments (MSAs) is a fundamental requirement in the analysis of protein sequences, allowing us to visu- alize conservation across protein families as well as unusual features of ...
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Sequence analysis and editing for bisulphite genomic sequencing projects
... or sequence electropherograms (without adaptive peak height adjustment), and then align them to a reference ...underlying sequence data surrounding the corresponding CpG dinucleotide, aligned to the ...
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Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
... either sequence or structure ...visualize sequence and secondary struc- ture ...RNA sequence and secondary structure alignments to a single 2D structure plot of the associated consensus struc- ...
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Noisy: Identification of problematic columns in multiple sequence alignments
... In order to assess whether the cyclic orderings obtained using QNet and NeighborNet reduce the fraction of unin- terpretable variation, we performed the following rand- omization experiment. Given an alignment, we ...
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SVM-based Automatic Annotation of Multiple Sequence Alignments
... performing alignments [5] between each possible pairs of ...of sequence is computed as the number of mismatched positions in an alignment divided by the total number of matched ...a cluster and 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 ...phylogenetic analysis and ...
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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 ...multiple ...
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BamView: visualizing and interpretation of next-generation sequencing read alignments.
... exome sequencing and ...by sequencing the genomes of closely-related isolates at an unprecedented scale [1] and to show that hom- ologous recombination has led to serotype switching and vaccine escape in a ...
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Kraken: ultrafast metagenomic sequence classification using exact alignments
... default, Kraken builds the database with k = 31, but this value is user-modifiable. Simulated metagenome data Although genuine metagenomic reads might provide the most realistic test of performance, such data would not ...
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Multiple sequence alignments of partially coding nucleic acid sequences
... quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence ...larger sequence heterogeneity compared to their ...
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DendroBlast: approximate phylogenetic trees in the absence of multiple sequence alignments
... of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred ...simulated sequence data we demonstrate that this method produces ...
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EvalMSA: a Program to Evaluate Multiple Sequence Alignments and Detect Outliers
... Multiple sequence alignments (MSAs) are essential instruments for prediction of protein structure and function, phylogenetic inference, and other tasks related to sequence ...such alignments ...
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Detecting species-site dependencies in large multiple sequence alignments
... also cluster the sites, was not avail- able anymore at the time of this ...Neither sequence-based nor site-based methods are on their own able to detect any recombination ...like sequence logos or ...
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