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Casalecchio di Reno, Italy

Piovesan D.,A+ Network | Luigi Martelli P.,A+ Network | Fariselli P.,University of Bologna | Zauli A.,BioDec srl | And 2 more authors.
Nucleic Acids Research | Year: 2011

We introduce BAR-PLUS (BAR+), a web server for functional and structural annotation of protein sequences. BAR+ is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13495736 protein chains also including 988 complete proteomes. Available sequence annotation is derived from UniProtKB, GO, Pfam and PDB. When PDB templates are present within a cluster (with or without their SCOP classification), profile Hidden Markov Models (HMMs) are computed on the basis of sequence to structure alignment and are cluster-associated (Cluster-HMM). Therefrom, a library of 10858 HMMs is made available for aligning even distantly related sequences for structural modelling. The server also provides pairwise query sequence-structural target alignments computed from the correspondent Cluster-HMM. BAR+ in its present version allows three main categories of annotation: PDB [with or without SCOP (*)] and GO and/or Pfam; PDB (*) without GO and/or Pfam; GO and/or Pfam without PDB (*) and no annotation. Each category can further comprise clusters where GO and Pfam functional annotations are or are not statistically significant. BAR+ is available at http://bar.biocomp.unibo.it/bar2.0. © 2011 The Author(s).

Bartoli L.,University of Bologna | Martelli P.L.,University of Bologna | Rossi I.,BioDec srl | Fariselli P.,University of Bologna | Casadio R.,University of Bologna
Current Protein and Peptide Science | Year: 2010

In this paper we aim at investigating possible correlations between the number of putative interaction patches of a given protein, as inferred by an algorithm that we have developed, and its degree (number of edges of the protein node in a protein interaction network). We focus on the human cell cycle that, as compared with other biological processes, comprises the largest number of proteins whose structure is known at atomic resolution both as monomers and as interacting complexes. For predicting interaction patches we specifically develop a HM-SVM based method reaching 71% overall accuracy with a correlation coefficient value equal to 0.43 on a non redundant set of protein complexes. To test the biological meaning of our predictions, we also explore whether interacting patches contain energetically important residues and/or disease related mutations and find that predicted patches are endowed with both features. Based on this, we propose that mapping the protein with all the predicted interaction patches bridges the molecule to the interactome at the cell level. To test our hypothesis we downloaded interaction data from interaction data bases and find that the number of predicted interaction patches significantly correlates (Pearson correlation value >0.3) with the number of the known interactions (edges) per protein in the human interactome, as contained in MINT and IntAct. We also show that the correlation increases (Pearson correlation value >0.5) when the subcellular co-localization and the co-expression levels of the interacting partners are taken into account. © 2010 Bentham Science Publishers Ltd.

Martelli P.L.,University of Bologna | D'Antonio M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo | Bonizzoni P.,University of Milan Bicocca | Castrignano T.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo | And 17 more authors.
Nucleic Acids Research | Year: 2011

Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256 939 protein variants from 17 191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPIanchor propeptides, transmembrane and coiledcoil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www .caspur.it/ASPicDB/. © The Author(s) 2010.

Piovesan D.,University of Bologna | Martelli P.L.,University of Bologna | Fariselli P.,University of Bologna | Profiti G.,University of Bologna | And 3 more authors.
BMC Bioinformatics | Year: 2013

Background: In the genomic era a key issue is protein annotation, namely how to endow protein sequences, upon translation from the corresponding genes, with structural and functional features. Routinely this operation is electronically done by deriving and integrating information from previous knowledge. The reference database for protein sequences is UniProtKB divided into two sections, UniProtKB/TrEMBL which is automatically annotated and not reviewed and UniProtKB/Swiss-Prot which is manually annotated and reviewed. The annotation process is essentially based on sequence similarity search. The question therefore arises as to which extent annotation based on transfer by inheritance is valuable and specifically if it is possible to statistically validate inherited features when little homology exists among the target sequence and its template(s).Results: In this paper we address the problem of annotating protein sequences in a statistically validated manner considering as a reference annotation resource UniProtKB. The test case is the set of 48,298 proteins recently released by the Critical Assessment of Function Annotations (CAFA) organization. We show that we can transfer after validation, Gene Ontology (GO) terms of the three main categories and Pfam domains to about 68% and 72% of the sequences, respectively. This is possible after alignment of the CAFA sequences towards BAR+, our annotation resource that allows discriminating among statistically validated and not statistically validated annotation. By comparing with a direct UniProtKB annotation, we find that besides validating annotation of some 78% of the CAFA set, we assign new and statistically validated annotation to 14.8% of the sequences and find new structural templates for about 25% of the chains, half of which share less than 30% sequence identity to the corresponding template/s.Conclusion: Inheritance of annotation by transfer generally requires a careful selection of the identity value among the target and the template in order to transfer structural and/or functional features. Here we prove that even distantly remote homologs can be safely endowed with structural templates and GO and/or Pfam terms provided that annotation is done within clusters collecting cluster-related protein sequences and where a statistical validation of the shared structural and functional features is possible. © 2013 Piovesan et al.; licensee BioMed Central Ltd.

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