Input
Nucleotide Query Seq(s)   Place your query file with nucleotide sequences in FASTA format.
Location on query sequence   Location on the query sequence in 1-based offsets (Format: start-stop).
Query strand(s)   Query strand(s) to search against database: Both strands
Plus strand
Minus strand
Translation table Select translation table:
Standart (1)
Vertebrate Mitochondrial (2)
Yeast Mitochondrial (3)
Mold, Protozoan, and Coelocoel Mitochondrial (4)
Invertebrate Mitochondrial (5)
Ciliate Nuclear and other (6)
Echinodermata Nuclear (9)
Euplotid Nuclear (10)
Bacterial and Plant Plastid (11)
Alternative Yeast Nuclear (12)
Ascidian Mitochondrial (13)
Flatworm Mitochondrial (14)
Blepharisma Macronuclear (15)
Chlorophycean Mitochondrial (16)
Trematode Mitochondrial (21)
Scenedesmus Obliquus Mitochondrial (22)
Thraustochytrium Mitochondrial (23)
Remote DataBaseSelect remote DB:
Non-Redundant - All GenBank, EMBL and DDBJ Non-Redundant sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences). WGS entries are also excluded. No longer "Non-Redundant".
EST - Database for entries from Estimated Sequence Tags (EST) division of GenBank, EMBL and DDBJ.
Human EST - H.Sapiens subset of Estimated Sequence Tags.
Mouse EST - M.Musculus subset of Estimated Sequence Tags.
Other EST - EST other than Human or Mouse.
GSS - Genomic Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.
HTGS - Unfinished High Throughput Genomic Sequences: phases 0, 1 and 2. Finished, phase 3 HTG sequences are in NR.
Patented sequences (PAT) - Nucleotides from the Patent division of GenBank.
Patented sequences - Nucleotides from the Patent division of GenBank..
Monthly Sequences (Month) - All new or revised GenBank, EMBL and DDBJ sequences released updated in the last 30 days.
Alu repeats - Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences.
STS - Database of GenBank, EMBL and DDBJ sequences from STS Division.
Chromosomic Sequences - Complete genomes, complete chromosomes, or concatenated genomic contigs from NCBI Reference Sequence Project.
Vector fragments (UniVec) - The UniVec non-redundant vector fragment sequences.
Whole Genome Shotguns (WGS) - Whole Genome Shotgun sequence assembly.
Custom - Specify the database of your interest.
Output
Result   Designates an output file for the search results.
Format   Pairwise (Default)
Query-anchored, showing identities
Query-anchored, no identities
Flat query-anchored, showing identities
Flat query-anchored, no identities
XML Blast output
Tabular
Tabular with comment lines
ASN, text
ASN, binary
Comma-separated values
BLAST archive format (ASN.1)
Options
Expectation value   Sets the threshold expectation value for keeping alignments.
This is the E from the Karlin-Altschul equation that describes how often an alignment with a given score is expected to occur at random. min=0, max=1000
Remote DB Genetic Code   Genetic code to use to translate database/subjects:
Standart (1)
Vertebrate Mitochondrial (2)
Yeast Mitochondrial (3)
Mold, Protozoan, and Coelocoel Mitochondrial (4)
Invertebrate Mitochondrial (5)
Ciliate Nuclear and other (6)
Echinodermata Nuclear (9)
Euplotid Nuclear (10)
Bacterial and Plant Plastid (11)
Alternative Yeast Nuclear (12)
Ascidian Mitochondrial (13)
Flatworm Mitochondrial (14)
Blepharisma Macronuclear (15)
Chlorophycean Mitochondrial (16)
Trematode Mitochondrial (21)
Scenedesmus Obliquus Mitochondrial (22)
Thraustochytrium Mitochondrial (23)
Matrix   Designates a protein similarity matrix.
This is used in all BLAST programs except blastn.
Matrices are sought in the following order: in the local directory, in the location specified in the .ncbirc file, in a local data directory, and finally, in the BLASTMAT environment variable (only on Unix systems). Other matrices included in the standard distribution include BLOSUM45, BLOSUM80, PAM30, and PAM70.
You can use custom matrix files, but it requires modifying the source code and defining the new matrix with all of its associated statistics for different affine gap combinations and recompiling the binary. Using these custom files isn't recommended because it requires the arduous task of calculating gapped values for lambda and maintaining a derivative branch of the source code.
Matrix selection:
BLOSUM62
BLOSUM45
BLOSUM80
PAM30
PAM70