 A
complete genome sequence of Plasmodium falciparum recently
published in Nature [2002 Oct 3; 419(6906): 498-511 - PubMed],
is available in GenBank.
A whole genome shotgun draft sequence of Anopheles gambiae was
also recently published in Science [2002 Oct 4;298(5591):129-149 - PubMed]
and is available in GenBank
and MapViewer.
A whole genome shotgun of Plasmodium yoelii yoelii was recently
published in Nature [2002 Oct 3; 419(6906): 512-519 - PubMed]
and is available in GenBank.
Nature - Malaria Genome Issue Oct. 3, 2002 - Free
Issue
http://www.nature.com/nature/malaria/
Science - Mosquito Genome Issue Oct. 4, 2002 - Free
Issue
http://www.sciencemag.org/feature/data/mosquito/index.shtml
Google
News Report
Anopheles
gambiae Genome Scaffold The first version of the Anopheles
gambiae genome scaffold was submitted into GenBank by Celera
Genomics and is now available through Map Viewer which also display
in tblastn alignments of all Drosophila
melanogaster proteins hitting the Anopheles scaffolds.
BLAST
access to the Anopheles gambiae genome is also available.
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?chr=agambiae.inf
NIH/NIAID Announcement: http://www.niaid.nih.gov/dmid/genomes/anopheles.htm
Trace
Arhive Database provides mega
blastable access to the raw data underlying all of the sequences generated
by the genome project. The An. gambiae genome trace data from Celera
Genomics is available.
http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?
NLM
Gateway allows users to search in multiple retrieval systems at the
U.S. National Library of Medicine (NLM). The current Gateway searches
MEDLINE/PubMed, OLDMEDLINE, LOCATORplus, AIDS Meetings, Health Services
Research Meetings, HSRProj, MEDLINEplus, and DIRLINE. See the Overview
for details.
cyclops
is a graphical program developed at the Sanger Centre for comparing a
whole chromosome assembly with the corresponding physical and/or genetic
maps. The user can move a graphical representation of selected contigs
around a window (called a "SandBox") to try to align them with
the physical and/or genetic maps of the chromosome. The program also shows
pUC bridges from the ends of contigs and allows the user to "tie"
pairs or groups of contigs together and move them around the SandBox as
a single unit. Cyclops is mainly used for the finishing process and there
is no annotation associated (Artemis is used for Annotation).
http://www.sanger.ac.uk/Software/sequencing/docs/harper/cyclops.shtml
For a Windows 95/98/NT/2000 "freestanding executable":
http://www.ncbi.nlm.nih.gov/Malaria/Cyclops/read_cyclops_win.html
AnoDB
is a database containing genomic/biological information on anopheline
mosquitoes with an emphasis on Anopheles gambiae, the prominent malaria
vector.
http://www.anobase.org/
The
Malaria Parasite Metabolic Pathways website coordinated by Hagai
Ginsburg is open to the public. http://sites.huji.ac.il/malaria/
The
Malaria Research and Reference Reagent Resource Center (MR4) provides
a central source of quality controlled malaria-related reagents and information
to the international malaria research community. Materials available to
qualified, registered users includes parasites, mosquito vectors, antibodies,
antigens, gene libraries, molecular probes and constructs, and human biological
material. http://www.malaria.mr4.org/mr4pages/index.html
The International
Journal for Parasitology, Volume 30/4 (April 2000) - Parasite Genome
- Thematic issue is freely available at the journal's Web site. http://www.elsevier.com/locate/parasitology
P.
yoelii Genome Database (TIGR/NMRC) :
TIGR/NMRC P. yoelii Genome Database TIGR and the Malaria Program
at the Naval Medical Research Center (NMRC) are collaborating on a research
program to provide low coverage sequencing of the P. yoelii genome
(http://www.tigr.org/tdb/edb2/pya1/htmls).
This project should identify over 90% of all the genes of the P. yoelii
genome.
Plasmodium
Proteome Classification and Analysis (WHO/EBI)- Web pages includes:
(No longer Maintained)
- a functional catalog of all current Plasmodium protein sequences
- a facility to search the Plasmodium protein sequence titles and
additional annotation for any string of letters and/or numbers
- a catalog of Plasmodium protein sequences placed in key biochemical
pathways
- a catalog of Plasmodium protein sequences placed in general protein/enzyme
classes
- a facility to search the Plasmodium protein sequences using a
user-defined motif
- a catalog of Pfam domains found in Plasmodium
http://www.ebi.ac.uk/parasites/PlasGN/Proteome/proteome.html
Plasmodium falciparum only version:
http://www.ebi.ac.uk/parasites/PlasGN/FalcipProteome/proteome.html
PlasmodiumDB
(University of Pennsylvania) - is the Malaria Genome Sequencing Project
Consortium Database maintained at the Univ ersity of Pennsylvania.
Resources that can be found at PlasmoDB include:
- Relational database queries, sequence retrieval, gene predictions (chromosome
2 and chromosome 3), expression analysis, DNA and protein feature identification,
gene ontologies, metabolic pathways, EST sequences and Blast analysis.
- Text-based search queries of Finished and Unfinished sequences, View
Blast-results, for each contig, download sequences (multiple formats)
and User-defined amino acid Motif Searches.
- GenePlot - platform-independent graphical browser, sequence retrieval.
Portable on CD-ROM.
- Links - other sites relevant to Plasmodium research.
http://plasmodb.org/
Protozoan
parasite search facilitie (WHO/EBI) - Motif search and general proteome
searches can now be performed against the following databases
- All Leishmania proteins
- Trypanosoma brucei proteins
- Trypanosoma cruzi proteins
- Leishmania major Friedlin proteins
- All kinetoplastids proteins
- All Plasmodium proteins
-Plasmodium falciparum proteins
The motif search facility can be found at:
http://www2.ebi.ac.uk/cgi-bin/parasites/motif_search.p
The more general keyword/text term search can be found at :
http://www2.ebi.ac.uk/cgi-bin/parasites/class_search.p
SCOPE
Malaria Research & Policy Web Forum was developed for research
scientists, field practioners, university instructors, policy makers,
and others who do work related to malaria. http://scope.educ.washington.edu/welcome/malaria/
Last updated: March 15, 2004
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