BLAST Help

General information

BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used separately for protein or DNA databases. and is best used for sequence searching, rather than for motif searching. Gramene provides BLAST facility for the Grasses. To search other datasets and access further information on BLAST resources, help document and BLAST 2.0 Release, please refer to http://www.ncbi.nlm.nih.gov:80/BLAST/.

BLAST methods

The NCBI BLAST family of programs includes:

blastp: Compares an amino acid query sequence against a protein sequence database.
blastn: Compares a nucleotide query sequence against a nucleotide sequence Database.
blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
tblastn: Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.
tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

Databases

Rice Protein sequences from SwissProt/TrEMBL. This data are kindly provided by their ftp site.
TIGR Rice Gene Index representing a clustering analysis of the public ally available rice ESTs. This data are kindly provided by TIGR FTP site.
Genbank Rice BAC/PAC Sequences All Rice Genomic clones sequenced by the International rice-sequencing project (IRSP).
Genbank Rice BAC ends
Genbank Rice ESTs
Genbank Barley ESTs
Genbank Maize ESTs
Genbank Wheat ESTs

Running Blast

To run Blast, a query sequence must be supplied by directly pasting the sequence in the text box. The examples of the sequence format are provided below. Select the appropriate blast program and dataset you want to query. Blast will run immediately and provide a summary table of results.

Examples:

FASTA format
>gi|11026061|gb|AU162662.1|AU162662 AU162662 Rice mature leaf Oryza sativa cDNA clone S20357, mRNA sequence CTCTCTTGGTTTCTCTCTCTAGCCATCGGCTGCCTCTCTCTCTCTCTCTCTCCTCGCTGCCCCATAGGTG GACGCGGGTCAACGGGCCGGTCGCCGGCGGGGCGGCTGCGGCGGCGAGAGGAGGTAGAAGCTCCGGCGAT CGCGAGGGCAGGCGGCGGGTTGGTGCGCTGCCGGCTTCGAGTTCGAGCGGGCGGGCCATGGGGAGGAACG GGAGCGTCAAGCGTACGTCGTCGTCGGGGGCGGCGGCGGCGTTCACGGCGAATCCCCGCGACTACCAGCT CATGGAGGAGGTCGGGTACGGGGCGCACGCCGTTCGTGTACCGCGCGCTGTTCGTCCCCAGGAACGACGT CGTGGCTGTCAAGTGCCTGGATCTCGATCAGCTTCAACAACAANATCGATGAAATCCAACGGGAGGCTCA AATCATGAGCTTGATAGAGCATCCTAATGTCATCAGGGCTTACTGCTCATTTGTTTGTTGAGCACAGCCT TTGGGGTAGTAATGCCATTTTATGACTGAGGGTTCATGTCTTGCACCTAATGAAGATTGCATATCCTGAT TGGTTTTCGAGGAAACTTGTTAATTTGGGCTCTAATTCTAAAGGAAAACACTTTAANGGCTTTTGGAAGT ACCTTCAAAAGGCAAGGACAAATCCATCGTGATGTCAAAGGCCGGCAATATCCCTTGTTGATAATGCTGG TATAGTGNAACT
Raw text format
CGCGAGGGCAGGCGGCGGGTTGGTGCGCTGCCGGCTTCGAGTTCGAGCGGGCGGGCCATGGGGAGGAACG GGAGCGTCAAGCGTACGTCGTCGTCGGGGGCGGCGGCGGCGTTCACGGCGAATCCCCGCGACTACCAGCT CATGGAGGAGGTCGGGTACGGGGCGCACGCCGTTCGTGTACCGCGCGCTGTTCGTCCCCAGGAACGACGT CGTGGCTGTCAAGTGCCTGGATCTCGATCAGCTTCAACAACAANATCGATGAAATCCAACGGGAGGCTCA AATCATGAGCTTGATAGAGCATCCTAATGTCATCAGGGCTTACTGCTCATTTGTTTGTTGAGCACAGCCT

Results Summary

Your BLAST request will run immediately and return results directly to your Web Browser in HTML format. The "Sequence" field will return the Accession numbers of the high scoring hits. The "Description" contains the brief description available from the FASTA format. By selecting the "Details" section it will take you directly to the BLAST alignment of the query sequence with the respective accession (sbjct) from the query database.