KAIKOBLAST System

Databases for use with BLAST

--------------------------- The following databases are currently or future available for BLAST searches: SW-WGS-RAMEN-CONTIGS Silkworm (p50, 'Daizo' strain) whole genome shotgun (WGS), Ramen assemble contigs SW-CDNA-PARTIAL-ALL Silkworm cDNA partial sequences from KAIKOcDNA database SW-CDNA-PARTIAL-CLUST Silkworm cDNA partial sequences (clustered) from KAIKOcDNA database


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 against a protein sequence database tblastn - Comparing a protein query sequence against a nucleotide 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 and JAPIO databases.


Parameters

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program

Specify the search program. Choose one of the following programs. blastn | blastp | blastx | tblastn | tblastx No default, YOU CANNOT OMIT THIS OPTION. Please confer "Available search programs" section.

datalib

Specify the databases in which homologous sequences are searched. Choose from following databases. SW-CDNA-PARTIAL-ALL | SW-CDNA-PARTIAL-CLUST SW-WGS-RAMEN-CONTIGS No default, YOU CANNOT OMIT THIS OPTION. Please confer "Databases for use with BLAST" section.

wordsize

Specify the word size. You had better not change the wordsize other than 11 for blastn. [integer] Default value: blastn=11, others=3 Maximum Minimum ----------------------- blastn 14 7 others 4 2

descriptions

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

alignments

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

expect

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

view

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 7 = XML Blast output Default value: 0

filter

Specify the filter query sequence (DUST with blastn, SEG with others). SEG program is for identifying and masking segments of low compositional complexity in amino acid sequences. [T/F] Default value: T

gap_open

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

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

dropoff

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

gi

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

extend_hit

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

gap_align (not available with tblastx)

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
NIAS DNA Bank