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B. Sherfudeen, II M.Sc., Bioinformatics Jamal Mohamed College
Map Viewer provides a graphical display of mapped Chromosomes,genes, markers and sequences.
Viewer having vertebrates, invertebrates, protozoa, plants and fungi genome map also.
Human Map Viewer provides a graphical view of the Human genome sequence maps.
Viewer to identify genes within a candidate region, and gene family.
► NCBI Map Viewer first released
Drosophila melanogaster genome in
Human genome map viewer
►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.
functions to report and download maps and annotated information.
to manipulate nucleotide sequence such as ModelMaker (for constructing mRNAs from putative exon sequences).
descriptions of the objects displayed on the maps.
Types of Maps
these maps, elements (genes, markers, clones) are localized on chromosomes using fluorescent or radioactive labeled probes.
FISHclone, Genes Cytogenetic, Morbid is types of Cytogenetic maps.
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:
maps are based on recombination frequency studies of genetic linkage in inheritance.
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.
Genethon, Marshfield. Sequence-Based Maps:
These maps are based on the human genome sequence in basepairs as generated by the Human Genome Project.
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:
maps are similar to genetic linkage maps,
treated cells are fused with a recipient cell line to create a library of hybrids with various donor chromosome fragments.
GeneMap99-GB, NCBI RH, Stanford G3 etc..
Maps and Gene location
Accessing the Genome
Information Resources (e.g. from Genomic Biology
Views: Graphically display of the complete genome as a set of chromosome
(e.g. from Entrez Genome, MapViewer Homepage/Hot
View: Shows one or more maps of interest for a selected chromosome at different level of resolution.
View: Displays the sequence data for a specific
chromosomal region and see the sequence.
from NCBI resources. Ex. Entrez Nucleotide, UniGene, UniSTS and LocusLink.
NCBI data resources:
Registry - Clone sequencing sequence status, STS content, and availability
- 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
- Locus-specific data for a subset of organisms with extensive links to related resources and sequence data
- Human from the same gene. - Unified, nonredundant database of sequence tagged sites (STSs)
►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)
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.
Selecting all matches in the summary table to having complete results for a particular chromosome.
Maps and Options window
Maps and Options:
Map Viewer provides zoom, navigation, and other map display controls.
all presents in Maps and Options window
Length: It is control of the number of labels on the Master map , and control of the diagram in the Thumbnail View.
add map’s to the display, select the map names and then click on ADD>>.
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