Title :
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
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;
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
DOI :
10.1109/ICCABS.2012.6182662
