NCBI-Human Genome Map Viewer

B. Sherfudeen, II M.Sc., Bioinformatics Jamal Mohamed College

Introduction
►NCBI

Map Viewer provides a graphical display of mapped Chromosomes,genes, markers and sequences.
►Map

Viewer having vertebrates, invertebrates, protozoa, plants and fungi genome map also.
►The

Human Map Viewer provides a graphical view of the Human genome sequence maps.
►Map

Viewer to identify genes within a candidate region, and gene family.
► NCBI Map Viewer first released

March 2000.
►URL:

Drosophila melanogaster genome in

http://www.ncbi.nlm.nih.gov/mapview

/

Human genome map viewer

Features
►Map ►a ►a

Viewer is a powerful tool because it provides:

mechanism to compare maps in different co-ordinate systems. strong query interface. for configuring the display.

►diverse

► multiple

functions to report and download maps and annotated information.
► tools

to manipulate nucleotide sequence such as ModelMaker (for constructing mRNAs from putative exon sequences).
► detailed

descriptions of the objects displayed on the maps.

Types of Maps
Cytogenetic Maps:
►In

these maps, elements (genes, markers, clones) are localized on chromosomes using fluorescent or radioactive labeled probes.
►Ideogram,

FISHclone, Genes Cytogenetic, Morbid is types of Cytogenetic maps.
►The

unit of this maps is chromosomal bands; for example, the gene EDN1 is located at 6p24.1 (chromosome 6, petit arm, band location 24.1).

Genetic Linkage Maps:
►These

maps are based on recombination frequency studies of genetic linkage in inheritance.
►The

standard unit of measurement for these maps is the cM (centimorgan): 1cM represents a 1% probability that a recombination has occurred between two positions on a chromosome.
►deCODE,

Genethon, Marshfield. Sequence-Based Maps:
These maps are based on the human genome sequence in basepairs as generated by the Human Genome Project.
►Position

of elements on the maps is identified by BLAST comparisons to the genomic sequence. ►Assemply, component, contig, STS, Unigene, Genbank RNA maps, Variation etc..

Radiation Hybrid Maps:
►These

maps are similar to genetic linkage maps,

►Radiation

treated cells are fused with a recipient cell line to create a library of hybrids with various donor chromosome fragments.
►GeneMap99-G3,

GeneMap99-GB, NCBI RH, Stanford G3 etc..

Maps and Gene location

Accessing the Genome
►Organism

Page)

Information Resources (e.g. from Genomic Biology

► Genome

Views: Graphically display of the complete genome as a set of chromosome
►Ideograms

Spots).

(e.g. from Entrez Genome, MapViewer Homepage/Hot

► Map

View: Shows one or more maps of interest for a selected chromosome at different level of resolution.
►Sequence

View: Displays the sequence data for a specific

chromosomal region and see the sequence.
►Links

from NCBI resources. Ex. Entrez Nucleotide, UniGene, UniSTS and LocusLink.

NCBI data resources:
►Clone

Registry - Clone sequencing sequence status, STS content, and availability
►dbSNP

- Single Nucleotide Polymorphisms (SNPs), polymorphisms, small-scale insertions/deletions, polymorphic repetitive elements
►RefSeq – NCBI ►UniGene

curated, non-redundant RefSeqs

- Computed clusters of cDNA and Expressed Sequence Tag (EST) sequences from the same gene, with tissue expression information and links to related resources
►LocusLink

- Locus-specific data for a subset of organisms with extensive links to related resources and sequence data
►OMIM

- Human from the same gene. - Unified, nonredundant database of sequence tagged sites (STSs)

►UniSTS

Query
►Query is unique identifier. ►It was identified specific database record. ►E.g., a sequence accession number or OMIM number or text term or

phrase or a gene symbol(BRCA2) or d53escriptor (p53-binding) or disease name.
►The Boolean AND operator is used.

E.g., a query for fanconi anemia will automatically interpretated as fanconi AND anemia

.

Map viewer summary results (query results)
►This

results from a query(600700) are displayed both graphically and in a summary table also.

Map viewer summary results:

►a) OMIM ►b)

(MIM) number was entered as a query search box and check it.

The red tick marks next to the chromosome diagram indicate where the results appear to be placed on the chromosome.
►c)

Selecting all matches in the summary table to having complete results for a particular chromosome.

Maps and Options window

Maps and Options:
►The

Map Viewer provides zoom, navigation, and other map display controls.
►It’s

all presents in Maps and Options window

.

►Page

Length: It is control of the number of labels on the Master map , and control of the diagram in the Thumbnail View.
►To

add map’s to the display, select the map names and then click on ADD>>.
►To

remove map’s from the display, select the map names in the Maps Displayed box and then click on <<REMOVE.

Find and Display a Gene

Find and Display a Gene:
By Gene Symbol:
►Give gene symbol Fragile X gene, FMR1 or FRAXA in search box. ►This gene symbol appears on Genes_seq, Genes_cyto, and

Marbid maps and then select all matches in Maps.

By Linkage to a disease: ►Genes that are linked to a disease OMIM are refered on morbid map.
►Searching foe disease name or phenotype ►E.g., FMR1

Association tools for Map viewer:
- Download/View Sequence/Evidence - Sequence viewer - Evidence viewer

Thank you

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