نتایج جستجو برای: sequence alignment

تعداد نتایج: 465792  

2010
İhsan Ömür BUCAK Volkan USLAN

DNA and protein are the fundamental biological sequences. DNA is a fundamental molecule that plays a vital role in the processes of life. Proteins synthesized by DNA in a cell are the building blocks of every living organism. There is a variety of reasons behind the alignment of biological sequences. Biological sequence alignment helps to discover functional and structural similarity of sequenc...

2016
Geetika Munjal Madasu Hanmandlu Deepti Gaur

In this paper various methods of sequence analysis which include the alignment based and alignment free methods of tree generation are reviewed and these find distance/similarity among the sequences of different species. Alignment free method based on tuple count and set theory is proposed and the results are compared with the guide tree obtained using alignment based method. The proposed metho...

Journal: :Bioinformatics 2007
Matthew Goode Allen G. Rodrigo

SUMMARY SQUINT is a sequence alignment tool, and combines both automated progressive sequence alignment with facilities for manual editing. The program imports nucleotide or amino acid sequence multiple alignment files in standard formats, and permits users to view two translations of the same multiple alignment simultaneously. Edits in one view are instantaneously reflected in the other, and t...

Journal: :Journal of integrative bioinformatics 2014
Alberto Montañola Concepció Roig Porfidio Hernández

Multiple sequence alignment (MSA), used in biocomputing to study similarities between different genomic sequences, is known to require important memory and computation resources. Nowadays, researchers are aligning thousands of these sequences, creating new challenges in order to solve the problem using the available resources efficiently. Determining the efficient amount of resources to allocat...

2012
Layal Al Ait Eduardo Corel Kifah Tout Burkhard Morgenstern

Background: Dialign is a DNA/Protein alignment tool for performing pairwise and multiple pairwise alignments through the comparison of gap-free segments (fragments) between sequence pairs. An alignment of two sequences is a chain of fragments, i.e local gap-free pairwise alignments, with the highest total score. METHOD: A new approach is defined in this article which relies on the concept of us...

1996
Michal Irani P Anandan Jim Bergen Rakesh Kumar Steve Hsu David Sarno

Recently, there has been a growing interest in the use of mosaic images to represent the information contained in video sequences. This paper systematically investigates how to go beyond thinking of the mosaic simply as a visualization device, but rather as a basis for an eecient and complete representation of video sequences. We describe two diierent types of mosaics called the static and the ...

Journal: :Bioinformatics 2013
Jamie R. Hill Charlotte M. Deane

MOTIVATION Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually made with programs designed for use on soluble proteins. Biological membranes have layers of varying ...

Journal: :Bioinformatics 2003
Michael Sammeth Burkhard Morgenstern Jens Stoye

A large number of methods for multiple sequence alignment are currently available. Recent benchmarking tests demonstrated that strengths and drawbacks of these methods differ substantially. Global strategies can be outperformed by approaches based on local similarities and vice versa, depending on the characteristics of the input sequences. In recent years, mixed approaches that include both gl...

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.

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