title: BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.
abstract: 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 13,495,736 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 10,858 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.
authors.affiliation: Department of Biology, Bologna Biocomputing Group, Bologna Computational Biology Network, Bologna, Italy.
authors.forename: Damiano
authors.initials: D
authors.lastname: Piovesan
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Martelli
authors.forename: Piero
authors.initials: P
authors.lastname: Fariselli
authors.forename: Andrea
authors.initials: A
authors.lastname: Zauli
authors.forename: Ivan
authors.initials: I
authors.lastname: Rossi
authors.forename: Rita
authors.initials: R
authors.lastname: Casadio
mesh_terms: D016000:Cluster Analysis; D020407:Internet; D058977:Molecular Sequence Annotation; D011487:Protein Conformation; D011506:Proteins / Q000502:physiology; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins