Poster: De novo expression fragment assembly from Spanning Trees (EAST)

Author

Zhang, Yuan ; Rao, Dhananjai ; Ozden, Mufit ; Mueller, Jens ; Kumar, Praveen Raj ; Liang, Chun ; Karro, John E.

Author_Institution

Depts. of Comp. Sci., Botany, Tech. Services, & Stat., Miami Univ., Oxford, OH, USA

fYear

2012

fDate

23-25 Feb. 2012

Firstpage

1

Lastpage

1

Abstract

In this poster we describe the methods underlying EAST, a novel algorithm based on Minimum Spanning Trees for the de novo assembly of short-read, traditional, and hybrid transcript-derived fragments sets, resulting in a tool that: consistently outperforms several popular tools on longer sequences (e.g. Sanger sequencing data and longer 454 sequences); is competitive against most tools on very short (e.g. 62 p Illumina) data; and is the most robust tool with respect to sequencing error. EAST can be installed and run through the PEACE GUI, with the implementation and code freely available at http://www.peace-tools.org.

Keywords

biological techniques; biology computing; genomics; molecular biophysics; molecular configurations; PEACE GUI; de novo expression fragment assembly; http://www.peace-tools.org; hybrid transcript-derived fragment set; minimum spanning tree; sequencing error; Assembly; Error analysis; Next generation networking; Robustness; Vegetation; Weight measurement;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Advances in Bio and Medical Sciences (ICCABS), 2012 IEEE 2nd International Conference on

Conference_Location

Las Vegas, NV

Print_ISBN

978-1-4673-1320-9

Electronic_ISBN

978-1-4673-1319-3

Type

conf

DOI

10.1109/ICCABS.2012.6182662

Filename

6182662