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 Drosophila melanogaster genome in

March 2000.

►URL: http://www.ncbi.nlm.nih.gov/mapview /
Human genome map viewer
 Features
►Map Viewer is a powerful tool because it provides:

►a mechanism to compare maps in different co-ordinate systems.

►a strong query interface.

►diverse for configuring the display.

► multiplefunctions to report and download maps and annotated

information.

► toolsto 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 Information Resources (e.g. from Genomic Biology
Page)

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

of chromosome

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

Spots).

► 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.

►Linksfrom 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)
►Thisresults 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.

►Toadd 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