An Eulerian path approach to DNA fragment assembly
نویسندگان
چکیده
منابع مشابه
An Eulerian path approach to DNA fragment assembly.
For the last 20 years, fragment assembly in DNA sequencing followed the "overlap-layout-consensus" paradigm that is used in all currently available assembly tools. Although this approach proved useful in assembling clones, it faces difficulties in genomic shotgun assembly. We abandon the classical "overlap-layout-consensus" approach in favor of a new euler algorithm that, for the first time, re...
متن کاملDNA sequence assembly and multiple sequence alignment by an Eulerian path approach.
We describe an Eulerian path approach to the DNA fragment assembly that was originated by Idury and Waterman 1995, and then advanced by Pevzner et al. 2001b. This combinatorial approach bypasses the traditional “overlap-layout-consensus” approach and successfully resolved some of the troublesome repeats in practical assembly projects. The assembly results by the Eulerian path approach are accur...
متن کاملAn Online approach to Overlap Detection for DNA Fragment Assembly
We consider the problem of estimating the number of sequences overlapping with a certain length from a large dataset of sequences. Such a problem is central to several challenging bioinformatics applications like DNA fragment assembly. A naive approach of calculating this numberis to perform an all-pairs comparison over the dataset. We propose an entirely different approach to tackle the proble...
متن کاملDNA Fragment Assembly: An Ant Colony System Approach
This paper presents the use of an ant colony system (ACS) algorithm in DNA fragment assembly. The assembly problem generally arises during the sequencing of large strands of DNA where the strands are needed to be shotgun-replicated and broken into fragments that are small enough for sequencing. The assembly problem can thus be classified as a combinatorial optimisation problem where the aim is ...
متن کاملAn Eulerian Path Approach to Global Multiple Alignment for DNA Sequences
With the rapid increase in the dataset of genome sequences, the multiple sequence alignment problem is increasingly important and frequently involves the alignment of a large number of sequences. Many heuristic algorithms have been proposed to improve the speed of computation and the quality of alignment. We introduce a novel approach that is fundamentally different from all currently available...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2001
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.171285098