ALPS

ALPS (alignment of pattern matrices score) uses information of a deep sequencing experiment, i.e. the relative positions and lengths of reads, to classify ncRNAs. ALPS makes no further assumptions e.g. about common structural properties in the ncRNA class and is yet able to identify ncRNA classes with high accuracy. Since scores are not biased towards a certain class of ncRNA, it can be used to detect novel ncRNA classes, as long as these unknown ncRNAs have a characteristic pattern of deep sequencing read lengths and positions.