In the light of acquiring whole genomes nowadays, we would like to know how far the analysis of functional relationships using genomes has attained during recent years. For example a simple classification problem at species level was attempted in some studies few years back. Are there any compuational methods developed for the same purpose or any other genome properties recently?
What are the recent algorithmic approaches being developed? Are there any mathematical models or methods developed to analyse the statistical parameters for whole genomes? And how should a whole genome information system be developed in cloud computing architecture?
I recently went through this paper
Article The Matrix Method of Representation, Analysis and Classifica...
I am looking into the possibility of using Paladin, to look into this question (functional characterization for genomes). While it was written for metagenomes, I have heard from users that this approach can be applied to genomes as well. Here's a link to the paper: Article PALADIN: Protein alignment for functional profiling whole me...
If you try it and it works please let me know! (I mostly teach, so research for me happens in somewhat geological time and if you discover this does or does not work I'd love to know).
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