Genomics | Bioinformatics | Theory & Simulation | Structural Genomics
From protein sequence to function and structure with BAR+
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, Rita Casadio*
*Corresponding author: Rita Casadio
Bologna Biocomputing Group, Bologna Computational Biology Network, University of Bologna, Bologna, Italy
F1000Posters 2011, 2: 1393 (poster) [ENGLISH]
Poster [1.90 MB]
Presented at
19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology 2011 (ISMB/ECCB),
17 - 19 Jul 2011, AFP/CAFA SIG (P000)
Functional annotation of protein sequences is one of the most important issues in annotation processes. To this aim we developed BAR, the Bologna Annotation Resource that is now updated (BAR+).
The method relies on the concept that sequences can inherit the same function(s) and structure from their counterparts, provided that they fall into a cluster endowed with validated annotations. BAR+ is based on a clustering procedure with the constraint that sequence identity (SI) should be ≥40% on at least 90% of the pairwise alignment overlapping (Coverage, Cov). Depending on the annotation types of the sequences within the cluster all new targets that fall into a cluster can inherit validated annotations by transfer. Following CAFA rules, predictions are carried out only for Molecular Function (MFO) and Biological Process Ontologies (BPO).
We aligned all the target sequences against BAR+ clusters that according to our constraints contain validated GO terms. When a sequence did not match any cluster, singletons (stand alone sequences in BAR+) were also used to transfer annotation provided that the criteria were also met. Out of total sum of 48,298 sequences, about 63% inherited validated MFO and BPO GO terms (with score 1). In the eukaryotic set 16,428 sequences were also annotated with Cellular Component (CCO) terms.
No relevant conflicts of interest declared.
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