Transitioning from LocusLink to Entrez Gene
Cancer Chromosomes: a New Entrez Database
HomoloGene: An Entrez Database with a New Look
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
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.
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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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.