Supplementary Material: Decoding Non-Unique Oligonucleotide Hybridization Experiments of Targets Related by a Phylogenetic Tree

Alexander Schliep, Sven Rahmann

Software

Update: 1/25/2007 As Sven Rahmann refuses to make his software Promide, which unfortunately is part of the whole pipeline, available there is currently no working implementation of the method.
Please accept my apologies. I am hard at work to create and test an alternative pipeline as soon as possible.
Alexander Schliep

The software implementing the code consists of Promide for probe selection and TPDC, the decoding software and a number of scripts. Promide is witheld by Sven Rahmann.

The decoder TPDC is an extension of the MCPD software available from http://algorithmics.molgen.mpg.de/MCPD/.


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Known Targets

We show the fraction of true targets under the top n ranked by posterior targets after decoding for the different data sets and errors. For example cherries-720.1571.3 followed by cher-0.05-0.05-3.0 indicates the 3rd sampled dataset for f+ = f- = 0.05, averaged over the 10 repeated hybridization simulations.

Unknown Targets


Note that exact refers to the parent of the unknown, parent to its grandparent, children to its siblings and childrenOrParent to either its siblings or its grandparent, which differs from the paper.

Mixed Targets


Note that exact refers to the parent of the unknown, parent to its grandparent, children to its siblings and childrenOrParent to either its siblings or its grandparent, which differs from the paper.

Sequence Data