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 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 Entrez Quiz Masthead | |
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.
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.
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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