BLAST program selection guide - Cromatina

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BLAST program selection guide Reference Proteins Zebrafish reference proteins generated by the NCBI RefSeq project. [Back to top] 5.10 Use the Plants genome BLAST pages to search against green plant genomes. This page accesses sequences from a limited number of green plants. For most of the organisms listed, only nucleotide sequences and blastn and tblastn searches are available. Genomic contigs as well as protein sequences are available for Arabidopsis thaliana and Oryza sativa, and matches are linked to MapView. Table 5.10.1 Plants Genome BLAST Database Content Database Name Arabidopsis thaliana (mustard) Avena sativa (Oat) Glycine max (soy bean) Hordeum vulgare (Barley) Oryza sativa (Rice) Oryza sativa indica (Indian Rice) Oryza sativa ssp. indica WGS contigs (not mapped) Tricicum aestivum (Wheat) Zea mays (Corn) Lycopersicon esculentum (Tomato) Mapped sequences from all listed plants Content Genome assembly, mRNAs, and Proteins Currently available genomic clones, GSS, and STS entries Currently available genomic clone, GSS, EST, and STS entries Currently available genomic clones, ESTs, GSSs, and STSs Currently available genomic clone, EST, GSS, htg, and STS entries WGS contig assemblies, mRNAs, and Proteins WGS contigs, not yet mapped Currently available genomic clone, EST, GSS, and STS entries Currently available genomic clone and EST entries Currently available genomic clone, GSS, EST, and STSentries All of the DNA sequences above. [Back to top] 5.11 The Nematode BLAST page. In this page, one can access the Caenorhabditis genome and the derivative databases. Matches are linked to MapView. In addition, sequence database for Caenorhabditis briggsae is also available (genomic sequences only). 5.12 The Yeast Genome BLAST page provides access to multiple yeast genomes. http://www.ncbi.nih.gov/staff/tao/BLAST_1.html (18 of 24)12/17/2004 12:36:22 PM
BLAST program selection guide This page provides access to different yeast genomes and their protein translations. Sequences of other yeast strains are also available in addition to that for Saccharomyces cerevisiae and Schizosaccharomyces pombe. The databases for the two well known strains can be searched individually or together. Hits are linked to MapView. All flavors of BLAST, with the exception of tblastx, are available. Table 5.12.1 Database list for Yeasts page Organism Sequence Databases Available Schizosaccharomyces pombe Genome, mRNAs, and Proteins Saccharomyces cerevisiae Genome, mRNAs, and Proteins Saccharomyces paradoxus NRRL Y-17217 Nucleotide only Saccharomyces mikatae IFO1815(MIT) Nucleotide only Saccharomyces mikatae IFO1815(WashU) Nucleotide only Saccharomyces bayanus MCYC623(MIT) Nucleotide only Saccharomyces bayanus MCYC623(WashU) Nucleotide only Saccharomyces castellii NRRL Y-12630 Nucleotide only Saccharomyces kluyveri NRRL Y-12651 Nucleotide only Saccharomyces kudriavzevii IFO 1802 Nucleotide only All YEAST Genomes Genomes, mRNAs, and Proteins Neurospora crassa Genome, mRNAs, and proteins Magnaporthe grisea Genome, mRNAs, and proteins Aspergillus nidulans Genome, mRNAs, and proteins All Species Genomes, mRNAs, and Proteins [Back to top] 5.13 Use the Insects BLAST page to search the Anopheles gambiae, Drosophila melanogaster, and Apis mellifera genomes. This page provides access to the genome scaffold of Anopheles gambiae (mosquito), Drosophila melanogaster (fruitfly), and Bombyx mori (silkworm/moth) chromosomes. The proteins translated from the genome annotation are also available. The data available for Anopheles gambiae is from a NIAID publicly funded project with the sequencing and assembly performed by Celera Corporation. The data for Drosophila melanogaster come from FlyBase. Hits are linked to corresponding MapViewer pages, providing additional information. Apis mellifera sequences were added recently, which has no MapViewer link yet. Organism Service Availability Databases BLAST searches MapViewer Link Drosophila melanogaster genomic, mRNA, Protein blastn, blastp, blastx, tblastn yes Anopheles gambiae genomic, mRNA, Protein blastn, blastp, blastx, tblastn yes Apis mellifera (honeybees) genomic, mRNA, Protein blastn, blastp, blastx, tblastn Drosophila pseudoobscura genomic only blastn, tblastn no Bombyx mori (silkworm/moth) genomic only blastn, tblastn no [Back to top] http://www.ncbi.nih.gov/staff/tao/BLAST_1.html (19 of 24)12/17/2004 12:36:22 PM
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