I would like to compare similarities of different allelic disorders based on HPO terms. As a first approach I just would like to select a few genes and look at how similar are the defined allelic diseases. My plan is to map OMIM disease clinical synopsis and map those to HPOs, and then apply some kind of similarity measure. However I couldn't yet identify a suitable software which I can use for calculating similarity for groups of HPO terms.
Thank you,
Peter
Dear Peter Balicza
These two are greatly helpful would shed light on your road.
Article Predicting disease-related phenotypes using an integrated ph...
Article HPOSim: An R Package for Phenotypic Similarity Measure and E...
To compare two gene fragments, we use standard algorithms of mathematical linguistics. For example, we look at two fragments (https://www.ncbi.nlm.nih.gov/nuccore/NM_002123 )
1 atcaggtccg agctgtgttg actaccactg ctttttccctt cgtctcagtt atgtcttgga
61 agaaggcttt gcggatcccc ggagaccttc gggtagcaac tgtcaccttg atgctggcga
121 tgctgagctc cctactggct gaggcagag actctcccga ggatttcgtg ttccagttta
We have a "similarity score" on the lines
L12 = 12.04159
L23 = 5.385165
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