Using the NCBI Map Viewer to Browse Genomic Sequence Data
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- Abstract
- Table of Contents
- Materials
- Figures
- Literature Cited
Abstract
This unit includes a basic protocol with an introduction to the Map Viewer, describing how to perform a simple text?based search of genome annotations to view the genomic context of a gene, navigate along a chromosome, zoom in and out, and change the displayed maps to hide and show information. It also describes some of NCBI's sequence?analysis tools, which are provided as links from the Map Viewer. The alternate protocols describe different ways to query the genome sequence, and also illustrate additional features of the Map Viewer. Alternate Protocol 1 shows how to perform and interpret the results of a BLAST search against the human genome. Alternate Protocol 2 demonstrates how to retrieve a list of all genes between two STS markers. Finally, Alternate Protocol 3 shows how to find all annotated members of a gene family. Curr. Protoc. Hum. Genet. 69:18.5.1?18.5.25 © 2011 by John Wiley & Sons, Inc.
Keywords: genome browser; genome assembly; genomic sequence; gene map
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Basic Protocol 1: General Navigation in the NCBI Map Viewer
- Alternate Protocol 1: BLAST Search Against the Genome
- Alternate Protocol 2: Using the NCBI Map Viewer to View a Region Between Two Markers
- Alternate Protocol 3: Using the NCBI Map Viewer to Identify All Members of a Gene Family in the Mouse Genome
- Commentary
- Literature Cited
- Figures
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryMaterials
Basic Protocol 1: General Navigation in the NCBI Map Viewer
Materials
Alternate Protocol 1: BLAST Search Against the Genome
Materials
Alternate Protocol 2: Using the NCBI Map Viewer to View a Region Between Two Markers
Materials
Alternate Protocol 3: Using the NCBI Map Viewer to Identify All Members of a Gene Family in the Mouse Genome
Materials
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GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryFigures
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Figure 18.5.1 The main entry point for the NCBI Map Viewer, showing the results of a query for ACHE on build 37.1 of the human genome. View Image -
Figure 18.5.2 The default Map View for the query ACHE. View Image -
Figure 18.5.3 The Evidence Viewer for exon 3 of ACHE. This window shows the alignment of the genomic contig NT_007933.15 with two RefSeq mRNAs (NM_######) and eleven GenBank mRNAs. View Image -
Figure 18.5.4 The Model Maker for ACHE, showing the exons contributed by 16 mRNAs (light blue) and 3 Gnomon gene predictions (hmm######). Together, these 19 sequences contribute 24 potential exons, numbered and shown in green. View Image -
Figure 18.5.5 The Maps & Options window, which allows the user to alter the default Map Viewer settings. View Image -
Figure 18.5.6 A customized view of the genomic context of the ACHE gene, using the maps selected in the Maps & Options window shown in Figure . View Image -
Figure 18.5.7 A zoomed‐in view of the display in Figure , showing the region around ACHE in detail. The variation (SNP) map is the master map. View Image -
Figure 18.5.8 The results of a megaBLAST search against the human “genome” database using the accession number for the ACHE mRNA RefSeq, NM_000665. View Image -
Figure 18.5.9 The Genome View of the results of the BLAST search shown in Figure , as shown in the Map Viewer results page. View Image -
Figure 18.5.10 The genomic context of the results of the BLAST search shown in Figure . View Image -
Figure 18.5.11 The genomic context of the region between RH markers RH46231 and RH71410. View Image -
Figure 18.5.12 The Summary of Maps from the region displayed in Figure . The summary highlights the fact that although there are 80 genes in this region, only 50 of them are labeled with a gene symbol. View Image -
Figure 18.5.13 A text view of the genes located between the two RH markers RH46231 and RH71410. This view was generated from the page shown in Figure by clicking on the link to Data as Table View. View Image -
Figure 18.5.14 The results of querying NCBI's mouse Map Viewer with ADAundefined [sym] NOT ADAMTundefined[sym] NOT ADAMDEundefined [sym] AND Gene[obj_type] AND genes[map_name]. This search results in all named members of the ADAM gene family in mouse. View Image -
Figure 18.5.15 An overview of the genomic context of the members of the ADAM gene family that map to mouse chromosome 14. View Image -
Figure 18.5.16 The Gene maps for the Celera mouse genome assembly and Reference mouse genome assembly are slightly different. The word “Celera” is written vertically near the top of the Celera Gene map. View Image
Videos
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