نتایج جستجو برای: multiple sequence alignment

تعداد نتایج: 1181017  

Journal: :CoRR 2014
J. Gerard Wolff

These notes pose a “proof challenge”: a proof, or disproof, of the proposition that For any given body of information, I, expressed as a one-dimensional sequence of atomic symbols, a multiple alignment concept, described in the document, provides a means of encoding all the redundancy that may exist in I. Aspects of the challenge are described.

2011
Roshanak Zilouchian Moghaddam Brian P. Bailey

Multiple Display Environments (MDEs) facilitate collaborative activities that involve the use of electronic task artifacts. Supporting interactions and infrastructures have matured in recent years, allowing researchers to now study how the use of MDEs impacts group work in controlled and authentic settings. This has created a need for tools to understand and make sense of the resulting interact...

Journal: :Proceedings. International Conference on Intelligent Systems for Molecular Biology 1996
Mark Gerstein Michael Levitt

We show how a basic pairwise alignment procedure can be improved to more accurately align conserved structural regions, by using variable, position-dependent gap penalties that depend on secondary structure and by taking the consensus of a number of suboptimal alignments. These improvements, which are novel for structural alignment, are direct analogs of what is possible with normal sequences a...

Journal: :Bioinformatics 2015
Bachir Balech Saverio Vicario Giacinto Donvito Alfonso Monaco Pasquale Notarangelo Graziano Pesole

Here we present the MSA-PAD application, a DNA multiple sequence alignment framework that uses PFAM protein domain information to align DNA sequences encoding either single or multiple protein domains. MSA-PAD has two alignment options: gene and genome mode.

Journal: :Bioinformatics 2003
Lusheng Wang Ying Xu

SUMMARY SEGID is a tool for finding conserved regions (regions of high scores) for a given (multiple) sequence alignment. It takes a (multiple) sequence alignment as its input and converts the alignment into a sequence of numbers, where each number is the alignment score of a column. Three algorithms are used to identify regions of high scores. A graphical interface is provided to present those...

Journal: :Bioinformatics 2006
Weizhong Li Adam Godzik

MOTIVATION Multiple sequence alignment is an important tool to understand and analyze functions of homologous proteins. However, the logic of residue conservation/variation is usually apparent only in three-dimensional (3D) space, not on a primary sequence level. Thus, in a traditional multiple alignment it is often difficult to directly visualize and analyze key residues because they are maske...

Journal: :Bioinformatics 2005
Timothy F. Oliver Bertil Schmidt Darran Nathan Ralf Clemens Douglas L. Maskell

Aligning hundreds of sequences using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. We present a new approach to compute multiple sequence alignments in far shorter time using reconfigurable hardware. This results in an implementation of ClustalW with significant runtime savings on a standard off-the-shelf FPGA.

Journal: :Applied Mathematics and Computer Science 2009
Jacek Blazewicz Piotr Formanowicz Pawel Wojciechowski

BAliBASE is one of the most widely used benchmarks for multiple sequence alignment programs. The accuracy of alignment methods is measured by bali score—an application provided together with the database. The standard accuracy measures are the Sum of Pairs (SP) and the Total Column (TC). We have found that, for non-core block columns, results calculated by bali score are different from those ob...

Journal: :Computers & chemistry 1999
Jaap Heringa

Multiple sequence alignment remains one of the most powerful tools for assessing sequence relateness and the identification of structurally and functionally important protein regions. In this work, two new techniques are introduced to increase the sensitivity of dynamic programming and to enable checks for alignment consistency: Profile-preprocessed and secondary structure-induced alignments. B...

2017
Frank J. Poelwijk Rama Ranganathan

Epistasis, or the context-dependence of the effects of mutations, limits our ability to predict the functional impact of combinations of mutations, and ultimately our ability to predict evolutionary trajectories. Information about the context-dependence of mutations can essentially be obtained in two ways: First, by experimental measurement the functional effects of combinations of mutations an...

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