Input
Protein Query sequence(s)	If the input file contains multiple sequences, BLAST will be run on each sequence in order, and the resulting output will contain concatenated BLAST reports.
Location on query sequence	Location on the query sequence in 1-based offsets (Format: start-stop).
Remote DataBase	Select 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: Pairwise aligning 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
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)
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
Perform gapped alignment	Performs gapped alignment. Setting this to OFF invokes the older, ungapped style of alignment. It is important to remember that gap penalties values depend on substitution matrix, so refer to NCBI for detailed information on subject!
Open Gap Cost	Initial penalty for opening a gap of length 0. The default gap costs for programs other than blastn depend on the scoring matrix.
Extend Gap Cost	The penalty for each gap character.