iQuant: A fast yet accurate GUI tool for transcript quantification

Author

Nguyen, Tin Chi ; Deng, Nan ; Xu, Guorong ; Duan, Zhansheng ; Zhu, Dongxiao

Author_Institution

Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA

fYear

2011

fDate

12-15 Nov. 2011

Firstpage

1048

Lastpage

1050

Abstract

Transcript quantification using RNA-seq is central to contemporary and future transcriptomics research. The existing tools are useful but have much room for improvement. We present a new statistical model, a fast yet accurate transcript quantification algorithm. Our tool takes RNA-seq reads in fasta or fastq format as input and output transcript abundance through a few mouse clicks. Our method compares favorably with the existing GUI tools in terms of both time complexity and accuracy. Availability: Both simulation data used for method comparisons and the GUI tool are freely available at http://asammate.sourceforge.net/.

Keywords

RNA; bioinformatics; biological techniques; data handling; graphical user interfaces; molecular biophysics; statistical analysis; GUI tool; RNA-seq; fasta format; fastq format; iQuant; statistical model; transcript abundance output; transcript quantification algorithm; transcriptomics research; Accuracy; Bioinformatics; Gene expression; Genomics; Graphical user interfaces; Mathematical model; Vectors; GUI; RNA-seq; Transcriptome quantification; alternative splicing; constrained least square;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on

Conference_Location

Atlanta, GA

Print_ISBN

978-1-4577-1612-6

Type

conf

DOI

10.1109/BIBMW.2011.6112556

Filename

6112556