Ncbi_map Viewer

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.

►diverse

for configuring the display.

► 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

curated, non-redundant RefSeqs

►UniGene

- 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.

►UniSTS

- Unified, nonredundant database of sequence tagged sites (STSs)

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

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

►b)

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 <
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