BAR 3.0

Features

BAR 3.0 is a web server for the functional annotation of protein sequences. The annotation process relies on a non-hierarchical clustering procedure of a BLAST all-against-all comparison of entire UniProtKB (SwissProt + TrEMBL) without fragments sequences. A graph scheme is adopted in which each protein is a node. An edge is established between two nodes if the two corresponding sequences share a BLAST hit that undergoes the following constraints:

• Sequence identity ≥ 40%

• Coverage of the alignment ≥ 90%

The coverage is defined as the ratio of the length of the intersection of the aligned regions on the two sequences and the overall length of the alignment (namely the sum of the lengths of the two sequences minus the intersection length). Clusters are the connected components of the graph and are disjointed (each sequence belongs only to one cluster).

Input

BAR 3.0 provides user different usage options:

• FASTA Sequence: the sequence will be aligned to the database.

• UniProt ID: if the accession is present in BAR 3.0, you will get a page with the cluster annotation.

• GO Term and PFAM code: if the term is statistically validated in at least one BAR 3.0 cluster, the output will show the list of matching clusters.

• PDB ID: if the PDB is associated to a sequence in a BAR 3.0 cluster, the output will show the list of such clusters.

• Ligand Code: if the ligand is associated to a PDB in a BAR 3.0 cluster, the output will show the list of such clusters.

• Organism ID: if the organism is associated to a sequence in a BAR 3.0 cluster, the output will show the list of such clusters.

Output

The cluster page shows different kind of information:

• Different statistics at the top.

• PDB section: a table listing all the PDB chains associated to it, along with UniprotKB accessions and ligands.

• PDB Complexes section: clusters containing sequences in complex with members of the result cluster.

• Protein-protein interactions section: clusters containing sequences associated in IntAct to members of the result cluster.

• GO Terms and PFAM annotations.

• KEGG Pathways section: KEGG pathways associated to sequences form the result cluster.