BLink Enhances Entrez Exploration of Protein Similarities

A popular feature of the Entrez search system is the ability to view similar sequences with a click of the Related Sequences button. A new service called BLAST Link (or BLink) transforms this feature from a simple one-dimensional listing of similarities into a panoramic display of graphical alignments‚ editable taxonomic trees‚ conserved protein classes‚ protein domains‚ and 3D structures.

Reached through BLink links at the head of protein records‚ the BLink summary page for a given protein sequence is centered around color-coded‚ graphical BLAST alignments to other proteins. This alignment view can be limited by taxonomic class or by BLAST score. Alternatives to the graphical alignment view include the standard BLAST taxonomy report and a Common Tree view. The Common Tree view allows a phylogenetic tree of the organisms represented in the alignments to be collapsed or expanded‚ and serves as an analysis aid.

Protein sequence similarities to structurally determined proteins can be shown through the 3D structures option‚ allowing for a smooth migration from 2D sequences to 3D structures or possible structural templates. The BLink summary page also offers the results of a CDD search against NCBI’s PFAM and SMART-derived library of protein domains. Links to the COGs database of protein groups‚ when applicable‚ allow access to information on the putative function and degree of conservation of similar proteins among 21 complete genomes.

BLink can also generate an Entrez report of all the proteins included in the BLAST alignment. In this manner‚ the protein neighbors of any protein in Entrez can be downloaded in a variety of formats for more extensive analysis.

Figure 1: BLink report for the human 54Kd signal recognition particle protein.

A sample BLink report for the 54Kd human signal recognition particle (SRP) is given in Figure 1. SRP is an essential cytoplasmic ribonucleoprotein complex that targets secretory proteins to the inner cell membrane of bacteria or the endoplasmic reticulum membrane of eukaryotes. SRPs are well-conserved and are represented in all kingdoms of life. The BLink report clearly indicates that 180 proteins similar to the 54Kd SRP protein are found in 81 different species from the archaea‚ bacteria‚ metazoa‚ fungi‚ plant‚ and other eukaryotic groups. By clicking on a taxonomic class‚ the graphical BLAST alignments can be tailored to include only those proteins from the particular taxa chosen. The alignment list can be restricted to sequences associated with Protein DataBank (PDB) 3D structures‚ SwissProt or RefSeq records‚ proteins from complete genomes‚ or COG members. Alignments can also be limited by BLAST score using a user-defined cutoff. The BLink report for any protein within an alignment can be reached by clicking on an individual gi number.

Access to BLink reports is also available from Entrez Genomes‚ AceView‚ SequenceView‚ and the COG pages. Links will soon appear as part of the protein BLAST output. For more detailed information‚ click on Help found at the top of any BLink report.

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