ORBL_tools: tools for measuring evolutionary conservation and constraint of 'ORFness' of an open reading frame.

ORBL measures cross-species evolutionary conservation and constraint on the "ORFness" of an open reading frame (ORF), without regard to conservation of the encoded amino acid sequence. It is intended to distinguish ORFs, such as regulatory uORFs, whose translation is functional, but which do not necessarily encode a functional peptide. It uses multi-species whole genome alignments to obtain the local alignment of the ORF in a particular clade, and then computes two scores, ORBLv and ORBLq. ORBLv measures conservation of ORFness by calculating the relative branch length of the phylogenetic tree of species in the alignment that have an intact orthologous ORF, i.e., in which there is an aligned ATG start codon, stop codon, and open reading frame. It is a number between 0 and 1, with larger numbers indicating more conservation. ORBLq measures evolutionary constraint on ORFness by calculating the quantile of its ORBLv score among the ORBLv scores of untranslated ORFs of the same biotype and similar length. It too is a number between 0 and 1, with larger numbers indicating more constraint. The number 1 - ORBLq can be thought of as a p-value, since it approximates the probability that a similar ORF would get the same or higher ORBLv score under the null hypothesis that its ORFness were not constrained.