NSMAP: A method for spliced isoforms identification and quantification from RNA-Seq
1 Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA
2 Department of Pathology, The Methodist Hospital Research Institute, Houston, TX 77030, USA
3 Weill Cornell Medical College, New York, NY 10065, USA
BMC Bioinformatics 2011, 12:162 doi:10.1186/1471-2105-12-162Published: 16 May 2011
The development of techniques for sequencing the messenger RNA (RNA-Seq) enables it to study the biological mechanisms such as alternative splicing and gene expression regulation more deeply and accurately. Most existing methods employ RNA-Seq to quantify the expression levels of already annotated isoforms from the reference genome. However, the current reference genome is very incomplete due to the complexity of the transcriptome which hiders the comprehensive investigation of transcriptome using RNA-Seq. Novel study on isoform inference and estimation purely from RNA-Seq without annotation information is desirable.
NSMAP provides a good strategy to identify and quantify novel isoforms without the knowledge of annotated reference genome which can further realize the potential of RNA-Seq technique in transcriptome analysis. NSMAP package is freely available at https://sites.google.com/site/nsmapforrnaseq. webcite