UFO: a web-server for ultra-fast functional profiling of large protein sequence collections
Functional profiling is a key technique to characterize and compare the metabolic potential of genomes and metagenomes. Up to now, large-scale estimation of profiles according to an assignment of sequences to functional categories is a computationally expensive task.
Based on new machine learning techniques for Pfam domain detection, the UFO web server for Ultra-fast Functional prOfiling allows to process large protein sequence collections instantaneously. In particular the server offers a quick overview on whole genome protein sequences. Besides the frequencies of Pfam and GO categories, also the sequence specific assignments to Pfam domain families are provided. A downloadable Perl script for postprocessing of UFO predictions can be used on a local computer for subsequent HMMER searches. For comparative analysis the profile divergences with respect to a large set of reference genomes are available.
For more information, please refer to:
P. Meinicke. UFO: a web server for ultra-fast functional profiling of whole genome protein sequences. BMC Genomics, 10:409, 2009. [WWW ]
If you use UFO results please cite the above publication.
NEW: UFO for fast taxonomic profiling of metagenomes using the Treephyler tool.
NEW: UFO now supports prediction of microbial phenotypes from whole genome protein sequences. The corresponding classifiers are based on training with Pfam protein domain profiles from 1032 prokaryotic organisms labeled according to NCBI annotation from May 2009.
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