DNA Sequence Assembly and Multiple Sequence Alignment by an Eulerian Path Approach

Abstract

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 accurate, and its computation is significantly more efficient than other assembly programs. As an extension, we use the Eulerian path idea to address the multiple sequence alignment problem. In particular, we have as a goal aligning thousands of sequences simultaneously, which is computationally exorbitant for all existing alignment algorithms. As a beginning, we focus on DNA sequence alignment. Our method can align hundreds of DNA sequences within minutes with high accuracy, and its computational time is linear to the number of sequences. We demonstrate its performance by alignments of simulated sequences and by an application in a resequencing project of Arabidopsis thaliana. Although having some weaknesses including aligning gap-rich regions, the Eulerian path approach is distinguished from other existing algorithms in solving either fragment assembly or multiple alignment

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

“…Although de Bruijn graph approaches are currently being used primarily for the purposes of assembly, they are a generally useful formalism for sequence analysis. In particular, they have been extended to efficient multiple-sequence alignment, repeat discovery, and detection of local and structural sequence variation (29,(32)(33)(34).…”

Design and development of DNA fragment assembly using IWP method

“…The process of assembly is then achieved by finding the Eulerian path in the de Bruijn graph. [8][9][10] Because of the benefit from de bruijn graph, in recent years, many software programs have been developed to merging the short reads fragment assembly in order to form the original sequences based on this approach as well. The most popular problems in sequencing technologies are to handle large amount of data produced as well as usually these short reads of DNA fragments have many overlaps.…”

“…Eulerian path is path which visits every edge exactly once. [2,10,13,14] A. Graph Construction The design methodology of this research is shown in figure below. It is realized by derivation of Verilog HDL code while the development is done in Xilinx ISE Design Suite 14.2.…”

Ανάπτυξη Υβριδικών Αλγορίθμων Με Βάση Μεθοδολογίες Δικτύων Για Τη Διερεύνηση Συσχετίσεων Σε Βιολογικά/Περιβαλλοντικά Δεδομένα

“…Τα δίκτυα αποτελούν πλέον σημαντικό εργαλείο και στο πεδίο της βιοπληροφορικής. Η εφαρμογή τους περιλαμβάνει μεταξύ άλλων τα δίκτυα γονιδίων και πρωτεϊνών (Goldberg et al, 2007), τη χρήση δικτύων με μορφή δένδρων για τη μελέτη της εξέλιξης (Huson and Bryant, 2006), τη μελέτη πρωτεϊνικών δομών (Amitai et al, 2004) και τη στοίχιση ακολουθιών (Zhang and Waterman, 2003).…”