| Input | |
| Query sequence(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 DataBase |
Remote DataBase selection:
Non-Redundant - All Non-Redundant GenBank CDS translations, PDB, SwissProt, PIR and PRF. Non-Redundant. SwissProt DB - Last major release of the SWISS-PROT protein sequence database (no updates). Patented Protein Sequence (PAT) - Patent Protein Sequence database. PDB Records - Sequences derived from the 3-Dimensional structure records from PDB. Monthly Sequences (Month) - All new or revised GenBank CDS translations, PDB, SwissProt, PIR and PRF released in the last 30 days. 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) |
| Show GI's in deflines | Shows GenInfo Identifier (GI) numbers in definition lines.
A GI is a unique numeric identifier assigned for a sequence in GenBank. A GI corresponds to an accession version pair. |
| 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 |
| 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. |