Enter coordinates for a subrange of the query sequence. The BLAST search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length.The range includes the residue at the To coordinate. more...
Use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences. The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format.
This title appears on all BLAST results and saved searches.
Enter one or more queries in the top text box and one or more subject sequences in the lower text box. Then use the BLAST button at the bottom of the page to align your sequences. To get the CDS annotation in the output, use only the NCBI accession or gi number for either the query or subject. Reformat the results and check 'CDS feature' to display that annotation.
Enter coordinates for a subrange of the subject sequence. The BLAST search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length.The range includes the residue at the To coordinate. more...
Select the sequence database to run searches against. No BLAST database contains all the sequences at NCBI. BLAST databases are organized by informational content (nr, RefSeq, etc.) or by sequencing technique (WGS, EST, etc.). more...
Enter organism common name, binomial, or tax id. Only 20 top taxa will be shown. [?]
Start typing in the text box, then select your taxid. Use the "plus" button to add another organism or group, and the "exclude" checkbox to narrow the subset. The search will be restricted to the sequences in the database that correspond to your subset.
You can use Entrez query syntax to search a subset of the selected BLAST database. This can be helpful to limit searches to molecule types, sequence lengths or to exclude organisms. more...
Enter a PHI pattern to start the search. PHI-BLAST may perform better than simple pattern searching because it filters out false positives (pattern matches that are probably random and not indicative of homology).
Maximum number of aligned sequences to display (the actual number of alignments may be greater than this).
Automatically adjust word size and other parameters to improve results for short queries.
Expected number of chance matches in a random model. more... Expect value tutorial
The length of the seed that initiates an alignment. more...
Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query. The algorithm is based upon //www.ncbi.nlm.nih.gov/pubmed/10890403
Assigns a score for aligning pairs of residues, and determines overall alignment score. more...
Reward and penalty for matching and mismatching bases. more...
Cost to create and extend a gap in an alignment. more...
Matrix adjustment method to compensate for amino acid composition of sequences. more...
Mask regions of low compositional complexity that may cause spurious or misleading results. more...
Mask repeat elements of the specified species that may lead to spurious or misleading results. more...
Mask query while producing seeds used to scan database, but not for extensions. more...
Mask any letters that were lower-case in the FASTA input. more...
Total number of bases in a seed that ignores some positions. more...
Specifies which bases are ignored in scanning the database. more...
Upload a Position Specific Score Matrix (PSSM) that you previously downloaded from a PSI-BLAST iteration. You may search a different database than that used to generate the PSSM, but you must use the same query. more...
Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.
Set the statistical significance threshold to include a domain in the model used by DELTA-BLAST to create the PSSM
Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented.