Some clarifications

[markcharder]

Dear Mike,

Thank you for the program, it's great (I realise it's been around for a while now!).

I've been reading through the documentation and the original publication here. My issue is that there seem to be a few discrepancies between the description of the algorithm in the paper and the description of the algorithm in the documentation of Cleaveland4.

I have a couple of questions about these discrepancies:

1. The publication says under '2.2 Input data': 'The pipeline requires three FASTA-formatted input datasets: degradome sequences (sequences are trimmed to the 5′-most 20 nts)'. Does this mean that the input degradome reads are automatically shortened by Cleaveland prior to analysis? On reading the code, this does not seem to be the case but I wanted to confirm.

2. The publication says under '2.3 Processing': 'Alignments are then scored according to a previously described scheme developed for plant miRNA/target pairings (Allen et al., 2005). All alignments with scores not exceeding the user-set threshold and having the 5′-end of the degradome sequence coincident with the 10th nucleotide of complementarity to the small RNA are retained.'. I don't see a threshold option for the Allen et al. score. Based on current documentation, it seems that the Allen et al. score criterion has been made non-default. The replacement seems to be a threshold for MFE ratio, as calculated by RNAplex, which is then used in calculation of P-values for candidate interactions. Can I confirm that this is correct?

Sorry if this is not quite the right forum for these questions - I don't have any issues with the code per se. Although a bit of clarification with respect to the publication might be useful in the documentation.

Many thanks for your help.

Mark