نتایج جستجو برای: alignment tools
تعداد نتایج: 339383 فیلتر نتایج به سال:
Multiple sequence alignments have primary role in several domains of modern molecular biology such as protein 3D structure/function prediction, phylogeny inference, molecular function, intermolecular interactions and many other common tasks in sequence analysis. Presently, many tools to construct multiple sequence alignments are available but none of them is accurate for all types of data sets....
Address: 1Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA, 2 Department of Genome Science, Life Science Division, Lawrence Orlando Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 4Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany, 5Departmen...
Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competiti...
Motivation Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Results Historian combines an efficient reimplementation of the...
After a brief account of a parallel corpus project involvingmany diverse languages and a summary of two previous evaluations of sentential alignment tools, results are presented from tests of three automatic aligners on English-Czech and French-Czech literary and legal texts, clean and noisy. The results confirm that an alignment tool may performwell on one type of texts and fail on another typ...
Today, RNA is well known to perform important regulatory and catalytic function due to its distinguished structure. Consequently, state-of-the-art RNA multiple alignment algorithms consider structure as well as sequence information. However, existing tools neglect the important aspect of locality. Notably, locality in RNA occurs as similarity of subsequences as well as similarity of only substr...
Digitalizing sheet music using Optical Music Recognition (OMR) is error-prone, especially when using noisy images created from scanned prints. Inspired by DNA-sequence alignment, we devise a method to use multiple sequence alignment to automatically compare output from multiple third party OMR tools and perform automatic error-correction of pitch and duration of notes. We perform tests on a cor...
We have developed new computational methods for displaying and analyzing members of protein superfamilies. These methods (MinRMS, AlignPlot and MSFviewer) integrate sequence and structural information and are implemented as separate but cooperating programs to our Chimera molecular modeling system. Integration of multiple sequence alignment information and three-dimensional structural represent...
Alignment to a genomic sequence is a common task in modern bioinformatics. By improving the methods used, significant amount of time and resources can be saved. We have developed a new genomic alignment search tool, called GAST, for sequences of at least 160 nt. GAST is many times faster than commonly used alignment tools BLAT and Mega BLAST. As the sizes of query sequences and the database inc...
The ability to perform genome-wide and cross-genome data analyses can dramatically reduce the time required for new biological discoveries. This raises important issues in bioinformatics database research involving data representations and data integration. Essential biological datatypes (such as sequence locations) and tools (such as the popular BLAST sequence alignment tools) are not supporte...
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