2 papers
cs.DS2014
Navigating in a sea of repeats in RNA-seq without drowning
Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet +3
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage inf…
q-bio.QM2013
A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data
Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot
We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alterna…