Available search programs

------------------------- blastn - Comparing a nucleotide query sequence against a nucleotide sequence database. blastp - Comparing an amino acid query sequence against a protein sequence database. blastx - Comparing a nucleotide query sequence translated in all reading frames aginst a protein sequence database. tblastn - Comparing a protein query sequence aginst a nucleocide sequence database dynamically translated in all reading frames. tblastx - Comparing the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that tblastx program cannot be used with the DNA, DDBJ, EMBL, GENBANK, JAPIO and CODON databases.




Specify the number of one-line descriptions. [integer] Default value: 100


Specify the number of alignments to show. [integer] Default value: 100


Specify the expected number of homologous sequences in the database. If you need to get more sequences with lower homology score, increase the "expect" value. If you need only sequences with very high homology scores, decrease the value. [Real] Default value: 10.0

match (blastn only)

Specify the reward for a nucleotide match. [integer] Default value: 1

mismatch (blastn only)

Specify the penalty for a nucleotide mismatch. [integer] Default value: -3


Specify the alignment view options. View parameter table: 0 = pairwise 1 = master-slave showing identities 2 = master-slave no identities 3 = flat master-slave, show identities 4 = flat master-slave, no identities 5 = master-slave no identities and blunt ends 6 = flat master-slave, no identities and blunt ends Default value: 0


The server filters your query sequence for low compositional complexity regions by default. Low complexity regions commonly give spuriously high scores that reflect compositional bias rather than significant position-by- position alignment. Filtering can elminate these potentially confounding matches (e.g., hits against proline-rich regions or poly-A tails) from the blast reports, leaving regions whose blast statistics reflect the specificity of their pairwise alignment. Queries searched with the blastn program are filtered with DUST. Other programs use SEG. Low complexity sequence found by a filter program is substituted using the letter "N" in nucleotide sequence (e.g., "NNNNNNNNNNNNN") and the letter "X" in protein sequences (e.g., "XXXXXXXXX").


Specify the cost to open a gap (zero invokes default behavior). [Integer] Default value: blastn = 5, others = See "gap_extend"


Specify the cost to extend a gap (zero invokes default behavior). [Integer] Default value: blastn = 2, others = See the following Sets of gap_open and gap_extend values (except blastn): gap_open gap_extend --------------------- 11 1(default) 10 1 9 2 8 2


Specify X dropoff value for gapped alignment (in bits) (zero invokes default behavior). [integer] Default value: 0


Specify GI's in deflines. [T/F] Default value: F


Specify the threshold for extending hits. [integer] Default value: 0


Perform gapped alignment [T/F] Default value: T

query_code (blastx only)

Specify Query Genetic code to be used in blastx translation of the query. Query genetic code table: 1 = Standard 2 = Vertebrate Mitochondrial 3 = Yeast Mitochondrial 4 = Mold Mitochondrial 5 = Invertebrate Mitochondrial 6 = Ciliate Macronuclear 9 = Echinodermate Mitochondrial 10 = Euplotid Nuclear 11 = Bacterial 12 = Alternative Yeast Nuclear 13 = Ascidian Mitochondrial 14 = Flatworm Mitochondrial 15 = Blepharisma Macronuclear Default value: 1