Malaria Genetics & Genomics

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Entrez

BLAST

OMIM

Taxonomy

Structure

Home General Info MGP Info Data Release What's New Features Meetings Site Search Plasmodium vivax Rodent Malaria Maps & Markers Genetic Maps Optical Maps Segregation Data Markers Electronic PCR Sequence Data BLAST GenBank BLAST Custom BLAST Enter Request ID Tutorial Epidemiology Taxonomy Tools Literature Search Research Projects Malaria Links Credits/Contacts FTP Access

Molecular Tools General Resources Single Sequence Similarity Search Tools Nucleotide Search/Analysis Tools Amino Acid/Protein Search/Analysis Tools Protein Domain Tools Gene Search/Analysis Tools Map Analysis Tools Structural Tools Biological Databases Useful Bioinformatics Guides General Resources: ExPASy Molecular Biology Server - provides many molecular resources with a special emphasis on proteins. EBI Tools List - database searching, browsing, and analysis tools. Single Sequence Similarity Search Tools NCBI BLAST (Basic Local Alignment Search Tool) family of tools is designed to support nucleotide and protein database analysis. BLAST BLAST2Seq Blast 2 Sequences against each other PHI-BLAST/PSI-BLAST Pattern Hit Initiated BLAST / Position Specific Iterated BLASTPosition Specific Iterated BLAST Malaria-specific GenBank BLAST Malaria-specific Custom BLAST EBI Sequence Similarity Searches FASTA3 homology searches WU-BLAST2 homology searches Bic_SW ScanPS - Similarity searches using Barton's algorithm PredictProtein server protein structure prediction and sequence analysis Nucleotide Search/Analysis Tools FASTA Compare a nucleic acid sequence to nucleotide sequence databases. Grail Analysis of the protein coding potential of a DNA sequence. Amino Acid/Protein Search/Analysis Tools: AllAllDB Search the All-Against-All Database of SwissProt. BCM Search Launcher General Protein Sequence/Pattern Searches BLOCKS Database of Highly-Conserved Protein Regions COGnitor Compare protein sequence against COG (Clusters of Orthologous Groups) database. (NCBI) - OLD MassSearch Search Swiss-Prot or EMBL databases by protein mass after digestion. ORF Finder The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool that finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes. The deduced amino acid sequence can be saved in various formats and searched against the sequence database using the WWW BLAST server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions. It is also packaged with the Sequin sequence submission software. (NCBI) ProfileScan Search a protein sequence against a profile database. PROPSEARCH Protein Identification in SwissProt and PIR using Amino Acid Composition. PROSITE-Search Compare a new protein sequence against all patterns stored in the PROSITE pattern database. Provides clues to the biological function of a new protein sequence. ScanProsite Scan a protein sequence or SWISS-PROT/ TrEMBL for the occurrence of patterns stored in the PROSITE database. TagIdent Selects proteins in the SWISS-PROT/TrEMBL database given pI and MW. Protein Domain Pfam at Wash Univ, St. Louis USA The Pfam database of protein domains and HMMs. SMART Simple Modular Architectural Research Tool for comparative sequence analysis. Gene Search/Analysis Tools BCM Gene Finder Splice sites, protein coding exons and gene models construction; Promotor and poly-A searches Frontier's in Bioscience Genefinder Map Analysis Tools: Electronic PCR (ePCR) - PCR-based sequence tagged sites (STSs) have been used as landmarks for construction of various types of genomic maps. These sites can be detected in DNA sequences by using "electronic PCR" (e-PCR), potentially allowing their map locations to be determined. (NCBI) Structural Tools Biological Structure Resource at Rutgers Univ. includes Nucleic Acid Database (structural information about nucleic acids), Structure Finder (provides access to macromolecular structure databases) BioMagResBank Repository for data from NMR spectroscopy on proteins, peptides, and nucleic acids. Cn3D Cn3D is a Web browser add-on that allows you to view three dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, MacOS, and Unix. The new version of Cn3D simultaneously displays structure, sequence, and alignment. (NCBI) DSSP Database of secondary structures of assignments for all protein entries in the Protein Data Bank (PDB). FSSP Fold classification based on structure-structure alignment of proteins (FSSP). Protein Data Bank International repository for the processing and distribution of three-dimensional macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR. Biological Databases: ATCC Cell lines database. BioMagResBank A Repository for data from NMR spectroscopy on proteins, peptides, and nucleic acids. Human 2-D PAGE Databases for proteome analysis in health and disease HyperCLDB Cell Lines Database. Swiss-2DPage Two-dimensional Polyacrylamide Gel Electrophoresis Database. ENZYME Enzyme nomenclature database ExPASy Proteomics tools List of proteomic tools Useful Bioinformatics Guides: Getting more from your sequence on the web: Guide to Sequence Analysis Tools Current Topics in Genome Analysis (NHGRI 2003 course) Current Topics in Genome Analysis - NIH Video Cast New User's Guide to the Human Genome at Nature Genetics - NIH Last updated: March 15, 2004. Disclaimer | Write to the Help Desk NCBI | NLM | NIH