In this issue

Transitioning from LocusLink to Entrez Gene

Cancer Chromosomes: a New Entrez Database

HomoloGene: An Entrez Database with a New Look

BLAST Link (BLink) to Protein Alignments and Structures

Debut of the HCT Database and Anthropology/Allele Frequencies in dbMHC

350kb Sequence Length Limit Removed by Sequence Database Collaboration

New Eukaryotic Genomes at NCBI

Environmental Samples Make Big Splash

HIV Protein-Interaction Database

e-PCR and Reverse e-PCR: Greater Sensitivity, More Options

New Organisms in UniGene

RefSeq Accession Numbers Get Longer as Rat Gets Last 6-digit Accession

Slots available for FieldGuidePlus Training Course Onsite at NCBI

RefSeq Release 6 on FTP Site

Exponential Growth of GenBank Continues with Release 142

Entrez Tools is a 'Hot Spot'

BLAST Lab: Using BLASTClust

New Microbial Genomes in GenBank

Entrez Quiz


BLAST Link (BLink) to Protein Alignments and Structures

Pre-computed sequence alignments, generated from routine all-against-all BLAST comparisons performed at NCBI, are available for each protein record in Entrez. The best 200 of these alignments can be displayed by clicking on the “BLink” link in the upper right-hand corner of Entrez protein reports. The BLink report for human MLH1 is shown in Figure 1.

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Figure 1: BLink report for the human MLH1 protein. Format controls are located at the top of the report with alignments, colored by the taxonomic origin of the database match, given in the lower section.

The report begins with a description of the query sequence, the sequence IDs of other entries in Entrez with identical sequences, and a set of controls, described below, used to customize the display. The alignments presented in the lower section of the report are depicted graphically and color-coded on the basis of the taxonomic origin of the aligned sequence. Each alignment is followed by its BLAST score, linked to a detailed alignment view, the accession number of the aligned sequence, linked to Entrez, and the GI number of the aligned sequence, linked to its own BLink report.

Customizing the Display

BLink reports can be customized using a combination of format buttons, taxonomic restriction controls, and a source database pulldown menu. Taxonomic and source database restrictions take effect when the “Select” button is pressed. Alignments may be sorted on the basis of sequence similarity to the query, the default, or by the taxonomic proximity of the source organisms using a link in the formatting area.

Six format buttons are used to select the display mode of the BLink report. The ‘Best Hits’ button displays a single line for each organism represented in the results, showing the alignment of the best hit in the organism group and a link, in the “N” column, to a Blink report limited to the group. A portion of a “Best Hits” display is shown in Figure 2.

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Figure 2 : "Best Hits" BLink report format indicating one alignment to a sequence from a synthetic construct and four alignments to sequences from Homo sapiens. A graphical depiction of the best alignment in each organism group is shown on the left.

The “Common Tree” button allows for the selective display of alignments to sequences arising from specific branches of the taxonomic tree. The related “Taxonomy Report” button lists the BLink results as a BLAST Taxonomy Report.

To limit the view to those sequences derived from structure records, press the “3-D Structures” button. In the “3-D Structures” display, shown in Figure 3, the dots are links to Con-served Domain and Cn3D structure displays.

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Figure 3 : BLink report limited to sequences derived from structures using the "3-D Structures" button.

The “CDD Search” button does not format the BLink report, but instead links to a precomputed conserved domain display for the query sequence.

The “GI” button links to the Entrez display of the protein sequences whose alignments are shown in the BLink report.

Taxonomic and Database Restrictions

Sequences derived from a taxonomic group may be selectively removed from the display by clicking on any of the color-coded taxon links; an “X” across the sequence count for the group indicates that the group will be removed from the display when the “Select” button is pressed. The BLink report can also be customized using the “Keep only” pulldown menu to limit the display to entries included in databases such as RefSeq, Protein Data Bank, SwissProt, COGs, and NCBI Complete Genomes.

Use BLink for Quick Insights into Protein Function

Because BLink reports are pre-computed it is possible to rapidly view a BLAST alignment without having to generate it. The graphical display of the aligned sequences provides a clear view of the distribution of conserved sequence blocks across taxonomic groups as an aid to understanding evolutionary and functional relationships. Added insight into protein function is provided by the CDD display of multiple sequence alignments for functional domains allowing one to evaluate position specific sequence conservation in the context of the biological function of the query protein. The “3D Structure” display provides a quick way to determine the availability of 3D structures to serve as modeling templates to use for further study.


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NCBI News | Fall/Winter 2002 NCBI News: Spring 2003