Multiple Sequence Alignments
SVM-based Automatic Annotation of Multiple Sequence Alignments
... of Multiple Sequence Alignments, this study explores an approach to 1) automate and reproduce manual editing, and 2) enable efficient and scalable Automatic ...of multiple alignments ...
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Core column prediction for protein multiple sequence alignments
... Results: We develop for the first time a predictor of column coreness for protein multiple sequence alignments. This allows us to predict which columns of a computed alignment are core, and hence ...
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AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments
... Multiple sequence alignments (MSAs) aim to organise a set of sequences by placing homologous residues into columns, and their accuracy affects subsequent steps in bioinformatic pipelines such as ...
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Noisy: Identification of problematic columns in multiple sequence alignments
... Sequence conservation in real data often varies dramati- cally along multiple sequence alignments ranging from constant sites to sequence positions that have effectively been ...
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KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences
... There are many reasons for constructing multiple sequence alignments (MSA), which form the backbone of comparative analyses and the starting point of phyloge- netic studies. Similarly, there are a ...
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Multiple Sequence Alignments in Linguistics
... Although multiple sequence alignments are broadly used in molecular biology, there is still no widely accepted objective function for evaluating the goodness of the multiple aligned strings ...
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AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences
... The AlignMiner Web interface was designed for maxi- mum simplicity and convenience of use. Users must log on with their e-mail to obtain a confidential space within the public environment (no registration is needed). ...
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RNAstrand: reading direction of structured RNAs in multiple sequence alignments
... a multiple sequence alignment, GU pairs in an evo- lutionary conserved stem provide information on the cor- rect reading direction since their reverse complement, AC, is not a canonical base ...a ...
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Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
... Here, we present an algorithm for the prediction of RNA-RNA interactions in existing multiple alignments of RNA sequences. Its rationale is based on the assumption that a non-negligible amount of the ...
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Multiple sequence alignment algorithms for the phylogenic analysis of chloroplast DNA
... align alignments exactly (AAE) using linear gap costs and under the sum of pairs objective ...“Aligning Alignments is the problem of finding an optimal alignment of the columns of two multiple ...
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Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures
... collecting multiple sequence alignments, con- sensus secondary structures and covariance models (CMs) for non-coding RNA families; and iv) RNAcen- tral, provided by collaborating groups (ENA, ...
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OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
... genome sequence data from vertebrate species provide unprece- dented opportunities for evolutionary analyses of protein coding ...in-frame multiple sequence ...in-frame alignments usually ...
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The Adaptive Evolution Database (TAED)
... coding sequence evolution is added, links to these datasets will be ...number. Multiple sequence alignments and phylogenetic trees corresponding to these entries can be obtained from EraGen ...
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Systematic search for putative new domain families in Mycoplasma gallisepticum genome
... Additional file 1: Supplemental Table ST1 Predicted putative new domain families. In our analysis, some of the unassigned regions shared homologues (at least 5 hits in PSI-BLAST search), but failed to associate with any ...
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14. D. Sivalingam, R. Rajendran and K. Anbarasan
... Pairwise sequence alignments were made with BLAST and multiple sequence alignments were also made with ...the sequence alignments, dendrograms were constructed using the ...
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Analysis of Chimpanzee History Based on Genome Sequence Alignments
... of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a ...
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Studies on DNA barcoding of sacred plant - Ficus religiosa L.
... Pairwise sequence alignments were made with BLAST and multiple sequence alignments are made with ClustalW, and based on the sequence alignments, dentrograms were ...
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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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A +1 ribosomal frameshifting motif prevalent among plant amalgaviruses
... Multiple sequence alignments for ORF2p from proposed and original plant amalgaviruses were also examined in detail for conserved residues including known RdRp motifs (Poch et ...strong ...
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Combining Multiple Alignments to Improve Machine Translation
... k-best alignments from a single alignment ...from alignments generated by different models (includ- ing MBR-based and refined ...the alignments in our work are generated by different models and their ...
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