NCBI Blastp accessing the NCBI Qblast system

Standard protein-protein BLAST

Takes protein (AA) sequences and compares them against the NCBI protein databases

Search for short and near exact matches

This search is similar to the standard protein-protein BLAST with the parameters set to optimize for searching with short sequences. A short query is more likely to occur by chance in the database. Therefore increasing the Expect value threshold, and also lowering the word size is often necessary before results can be returned. Low Complexity filtering has also been removed since this filters out larger percentage of a short sequence, resulting in little or no query sequence remaining. Also for short protein sequence searches the Matrix is changed to PAM-30 which is better suited to finding short regions of high similarity.

Parameters Setting

[COMPOSITION BASED STATISTICS] Do search with tweak parameter set to true,  learn moreThis will automatically perform a gapped alignment, so using UNGAPPED_ALIGNMENT also is unnecessary and will trigger a warning message from NCBI rather than generating results.

• Value    : yes, no
• Default : yes

[CDD_SEARCH] Compares protein sequences to the Conserved Domain Database. The CDD is a database containing a collection of functional and/or structural domains derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI. For more information please see the CDD homepage

• Value    : yes, no
• Default : yes

• Value    : see  protein databases
• Default : nr

[EXPECT] The statistically significant expectation value.  If the statistical significance ascribed to a match is greater than the E value, the match will not be reported.  Lower E values are more stringent, leading to a fewer chance matches being reported. Learn more

• Value    : double type value
• Default : 10.0

[ENTREZ_QUERY] Entrez query to limit Blast search

• Value    : Entrez query format
• Default : Empty

[FILTER] Sequence filter identifier

• L for Low Complexity
• R for Human Repeats
• m for Mask for Lookup

[GAP_OPEN_COSTS] Gap open costs

• Value    : integer values
• Default : 5 for nuc-nuc, 11 for proteins, non-affine for megablast

[GAP_EXTEND_COSTS] Gap extend costs

• Value    : space separated float values
• Default : 2 for nuc-nuc, 1 for proteins, non-affine for megablast

[HITLIST_SIZE] Number of hits to keep

• Value    : integer value
• Default : 20

[LCASE_MASK] Enable masking of lower case in query

• Value    : yes, no
• Default : no

[MATRIX_NAME] A key element in evaluating the quality of a pairwise sequence alignment is the "substitution matrix", which assigns a score for aligning any possible pair of residues.  The matrix used in a BLAST search can be changed depending on the type of sequences you are searching with (see the BLAST Frequently Asked Questions).  More information on BLAST substitution matrices

• Value    : Valid matrix name
• Default : BLOSUM62

OTHER_ADVANCED

    *[DROPOFF] Blast extensions in bits (default if Zero), not applicable for megablast

• Value    : integer value
• Default : 20 for nuc-nuc, 7 for other programs

    *[X_DROPOFF] X dropoff value for gapped alignment (in bits)

• Value    : integer value
• Default : 30 for nuc-nuc (blastn and megablast), 15 for other programs

    *[FIANL_X_DROPOFF] Final X dropoff value for gapped alignment (in bits), not applicable for megablast

• Value    : integer value
• Default : 50 for nuc-nuc (blastn), 25 for other programs

    *[DB_LENGTH] Effective length of the database (use Zero for real size)

• Value    : real value
• Default : 0

[PROGRAM] Blast program name

• Value    : blastn, blastp, blastx, tblastn, tblastx
• Default : blastn

[QUERY_BELIEVE_DEFLINE] Whether to believe defline in FASTA query

• Value    : yes, no
• Default : no

[QUERY_FROM] Start of subsequence (one offset)

• Value    : integer value
• Default : 0

[QUERY_TO] End of subsequence (one offset)

• Value    : integer value
• Default : 0, that means not to use subsequence

[SEARCHSP_EFF] Effective length of the search space 

• Value    : integer value
• Default : 0

[SERVICE] Blast service which needs to be performed

• Value    : plain, psi, phi, rpsblast, megablast
• Default : plain

[THRESHOLD] Threshold for extending hits

• Value    : integer value
• Default : ???

[UNGAPPED_ALIGNMENT] Should the ungapped alignment be performed? Note that this parameter should not be set to TRUE or YES when using COMPOSITION_BASED_STATISTICS since that will automatically perform a gapped alignment; if this parameter is on, it will trigger a warning message from NCBI rather than generating results.

• Value    : yes, no
• Default : no

[WORD SIZE] The search word size

• Value    : integer value; 2 or 3 for proteins, 7 or greater for nuc
• Default : 3 for proteins, 11 for nuc-nuc, 28 for megablast