|Plasmodium falciparum genome data and search tips||Revised September 15, 2003|
The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Plasmodium falciparum (malaria), and the search tips specific to that organism. You can also return to the Plasmodium falciparum genome view search page. The Map Viewer home page allows you to search the genome data of any organism represented in MapViewer.
|Scope of Data|
The Map Viewer provides a graphical view of malaria data from a variety of sources, including assembled sequence data, gene annotations, and genetic linkages for Plasmodium falicparum. The genome data were prepared by the Malaria Genome Sequencing Consortium, including:
The malaria genome sequence (both Plasmodium y. yoelii shotgun sequences and Plasmodium falciparum complete finished sequence) as submitted to GenBank is available at the Entrez Genome Malaria BLAST page. Prior release and unsubmitted sequence data to GenBank is available from the NCBI Malaria Genetics & Genomics Custom BLAST page.
|Additional resources are accessible from the Malaria Genetics and Genomics site and the PlasmoDB, GenBank sequence data for Plasmodium falciparum can be retrieved through the Taxonomy Browser. We will regularly provide updates to the Plasmodium falciparum MapViewer as maps and data becomes available.|
|The available maps for Plasmodium falciparum include:|
|Contig||The chromosome (Chr) sequence map shows the genomic chromosome assembled from the components. The chromosome sequence map is analogous to the contig map of organisms such as human and mouse. The chromosome sequence map has an accession in the format NC_XXXXXX, and is assembled from finished (phase 3) high-throughput genomic sequence (HTGS) records that were submitted by the sequencing centers.|
|Component||The component (Comp) map provides the tiling path of GenBank accessions (finished, phase 3 HTGS records) used to build the chromosome sequence map.|
|Gene||Genes that have been annotated on the chromosome sequence map. This includes known and putative genes placed as a result of alignments of reference sequence proteins (NP_XXXXXX) to the chromosome sequence using blastx. The default view uses the gene name that was provided by the sequencing centers (e.g. MALXXXX or PFXXXX).|
Alignment of Plasmodium yoeli proteins to the
Plasmodium falciparum genomic sequence.
BLAST was used to compare proteins from the complete
genome of P. falciparum to the preliminary annotation
of whole shotgun sequences of P.yoelii, and to
identify the reciprocal best hits.* The P.yoelii
proteins are positioned in order of their best matches in
P. falciparum, which doesn't necessarily reflect
the actual order of the proteins in P.yoelii genome.
In addition, the percent identity shown in the "alignment"
column of the display (when the Py protein map is the master map) is for the local alignment region,
not for the complete protein sequence.
* Reciprocal best hits are proteins from different organisms that are each other's top BLAST hit, when the proteomes from those organisms are compared to each other. For example, proteins A-Z in organism 1 are compared against proteins AA-ZZ in organism 2. If protein A has a best hit to protein RR, and RR's best hit, when it is compared to all the proteins in organism 1, also turns out to be protein A, then A and RR are reciprocal best hits. However, if RR's best hit is to B rather than to A, then A and RR are not reciprocal best hits.
|STS||Placement of STSs from UniSTS onto the chromosome sequence map, using Electronic-PCR (e-PCR).|
|Genetic Linkage Maps|
The malaria genetic linkage map from (Su et a. 1999), using markers and map information available from the NCBI Malaria Genetics and Genomics site. Microsatellite markers are position based on their recombination rates.
|Types of objects and maps on which they can be found|
|Components of Sequence Assembly|
| The Plasmodium falciparum data are searchable with the following
types of terms:
Search terms can also be truncated or include wild cards, as explained in the truncation section of the general Map Viewer Help document. For example, the following searches will retrieve the merozoite surface protein (MSP1) gene:
| As noted in the Search
By Position section of the Entrez Map Viewer general help document,
there are three main ways to search by map position from the Map View
of a chromosome:
It is not necessary to enter a value in both Region text boxes. If you enter a value only in the upper box, the Map Viewer will display the region of the chromosome starting from that point and ending at the bottom of the chromosome. If you enter the value only in the lower box, the Map Viewer will display the region of the chromosome starting at the top of the chromosome and ending at the value you entered.
|Constructing URLs that link to Map Viewer|
|If you would like to create WWW links to the Map Viewer, the instructions for constructing URLs are given in the general Map Viewer Help document. You can construct URLs that either perform a search or display a specific mapped object or chromosomal region.|
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