The databases to run the sequence similarity search against. Multiple databases can be used at the same time
Provide sequence in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP, or UniProtKB/Swiss-Prot (Protein only) format directly, or upload a file.
blastp: protein-protein search. blastx: nucleotide query against a protein database. blastn: nucleotide-nucleotide search. tblastn: protein query against a nucleotide database. tblastx: six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database
Specify one or more TaxIDs (included) so that the BLAST search becomes taxonomically aware. Taxonomy IDs need to be separated by a comma (no space) and only 'UniProtKB' and 'ENA' databases currently work with Taxonomy IDs.
Specify one or more excluded TaxIDs (excluded) so that the BLAST search becomes taxonomically aware. Taxonomy IDs need to be separated by a comma (no space) and only 'UniProtKB' and 'ENA' databases currently work with Taxonomy IDs.
The substitution matrix used for scoring alignments when searching the database.
The match score is the bonus to the alignment score when matching the same base. The mismatch is the penalty when failing to match.
Penalty taken away from the score when a gap is created in sequence. Increasing the gap openning penalty will decrease the number of gaps in the final alignment.
Penalty taken away from the score for each base or residue in the gap. Increasing the gap extension penalty favors short gaps in the final alignment, conversly decreasing the gap extension penalty favors long gaps in the final alignment.
Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.
Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather than meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.
The amount a score can drop before gapped extension of word hits is halted
Maximum number of match score summaries reported in the result output.
Maximum number of match alignments reported in the result output.
Specify a range or section of the input sequence to use in the search. Example: Specifying '34-89' in an input sequence of total length 100, will tell BLAST to only use residues 34 to 89, inclusive.
Maximum number of HSPs alignments to keep for any single query-subject pair.
This setting that tells the program the perform optimised alignments within regions involving gaps. If set to true, the program will perform an alignment using gaps. If it is set to false, it will report only individual HSP where two sequence match each other, and thus will not produce alignments with gaps.
Formating for the alignments
Use composition-based statistics.
Word size for wordfinder algorithm.
Query Genetic code to use in translation