The PubChem BioAssay Database contains target specific biologically active small molecules and their bioactivity results. This blast page allows you to blast a given set of protein sequences to find matches to those protein targets in the PubChem BioAssay database. Matching hits will have "dose-response" curve gif icons which links to corresponding entries in Entrez PCAssay. Different from text query on Entrez PCAssay database, this page provides a way to search and retrieval of BioAssay data through protein sequence similarity search using BLAST. PubChem BioAssay content can be searched and accessed from http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay and http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi
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.
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...
Enter organism common name, binomial, or tax id. Only 20 top taxa will be shown. [?]
Select from the list or choose “Custom” to enter the name of an organism. The search will be restricted to the sequences in the database which are from the organism selected.
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...
The length of the seed that initiates an alignment. more...
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.
BLAST Basic Local Alignment Search Tool
BLAST Basic Local Alignment Search Tool
