PubMed Nucleotide Protein Genome Structure Taxonomy

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.

  1. Scope of Data
  2. Available Maps
  3. Types of mapped objects, and maps on which they can be found
  4. Constructing queries
  5. Constructing URLs

Scope of Data back to top

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.

Available Maps back to top

The available maps for Plasmodium falciparum include:

Map Name Description
Sequence Maps back to top

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).

Py Protein 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 back to top

NIAID Genetic

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 back to top

Components of Sequence Assembly back to top

GenBank Accessions back to top

Genes back to top

  • Sequence maps
  • Genetic Linkage maps
    • Genetic (Su et. al 1999 Science map)

STSs back to top

  • Sequence maps
  • Genetic linkage maps
    • Genetic (Su et. al 1999 Science map)

Constructing queries back to top

Searchable Terms back to top

Text terms back to top

The Plasmodium falciparum data are searchable with the following types of terms:
  • gene symbol (e.g. rifin)
  • gene name (e.g. PFB0010w)
  • marker name (e.g. C2M18)
  • marker alias
    Sometimes two or more marker names refer to the same primer pair, and are therefore considered synonyms or "aliases." In such cases, any one of the terms will retrieve the marker.
  • RefSeq protein accession (e.g. NP_473134)
  • RefSeq protein product description (text words)
    e.g., a search for *actin* will retrieve map objects containing that word in their descriptions. At the present time, the words should be surrounded by asterisks. That will retrieve records which contain those words in any position within a phrase. In searches for multiple words, asterisks can be placed at both ends of the word group (e.g., *transcription factor*). That will retrieve records containing those words adjacent to each other, in any position within a phrase. If asterisks are also placed between the words (e.g., *transcription*factor*), the adjacency requirement is removed. The use of asterisks around words is a temporary measure until the text searching function is enhanced. Future plans also include enabling the use of Boolean operators (AND, OR, NOT) in text word searches.

Truncation back to top

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:

  • MSP1
  • MSP?   (each question mark represents a single character; multiple question marks can be used)
  • MSP*   (an asterisk represents zero to many characters)

Map Positions back to top

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:

  1. enter a range of interest in the Region text boxes in side bar
  2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
  3. click on a region of interest in the enlarged Map View of the chromosome

For Plasmodium falciparum, the following types of map positions can be entered in option 1:

  • marker names - you can enter marker names or alternate marker names (aliases) to display a region of the chromosome between mapped elements. Note that both mapped elements must be present on the maps that share the same coordinate system in order for the range search to work For example, if the Genetic Map is the Master Map, then you can enter the microsatellite marker names to get the range of display based on the marker names.
  • gene symbols
  • numerical positions - It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map (bases or centiMorgans). For example:
    • cM - if the master map is a genetic linkage map, the search program interprets the region number as a centiMorgan (cM) unit (e.g., 1 or 12 or 12.5)
    • base pairs - if the master map is a sequence map, you can enter base pair positions in the following types of formats:
      1000000 or 1,000,000 or 1M or 1000K or 1.1M or 1.2K

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 back to top

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.

Questions or Comments?
Write to the NCBI Service Desk