Search Statistics in Result Report

This is an example of the statistical details that are appended to a CAS Registry^SM BLAST^® result (in this case, a BLASTn result).

Report Section	Explanation
Search Statistics
Lambda	A statistical parameter used in calculating BLAST^® scores that can be thought of as a natural scale for scoring system. The value lambda is used in converting a raw score (S) to a bit score (S'). K A statistical parameter used in calculating BLAST^® scores that can be thought of as a natural scale for search space size. The value K is used in converting a raw score (S) to a bit score (S'). H The relative entropy of the target and background residue frequencies (Karlin and Altschul, 1990). H can be thought of as a measure of the average information (in bits) available per position that distinguishes an alignment from chance. At high values of H, short alignments can be distinguished by chance, whereas at lower H values, a longer alignment may be necessary (Altschul, 1991).
Gap Penalties	See Gap cost.
Number of Hits to DB	Values for the various steps in this BLAST^® search leading to the identification of HSPs.
Number of Sequences
Number of extensions
Number of sequences better than 10.0
Number of successful extensions
Length of query	Number of characters in search sequence.
Length of database	Number of letters in database at time of search.
Effective HSP length	Calculated values for database size, query size, etc. used in this BLAST^® search
Effective length of query
Effective length of database
Effective search space
Effective search space used
T	Neighborhood word score threshold. This generates all words of length W that yield a score of at least T when aligned with some word of length W from the query sequence. BLASTn: The value of T in a BLASTn result will be zero because BLASTn allows only identical matches for the initial word.
A	A "distance" within which two initial word hits (HSPs) must occur. BLASTn: Because BLASTn does not look for two words (HSPs) initially, this parameter is not used and the value is indicated as zero.
X1 . . . n:	Extension of alignment can result in a score drop before extra matches appear to raise the score again and compensate for the drop. The X value dictates when to stop the exploration. Example: The three Xs in the gapped BLAST^® program indicate: Dropoff for the ungapped extension (the HSP). Dropoff parameter used in the first gapped extension. Dropoff parameter used n the second (final) gapped extension.
S1 and S2	Cutoff scores for the maximal-scoring segment pair (MSP) and multiple HSPs, respectively. Pairwise comparisons scoring below these cutoff scores are ignored. Cutoff scores: Cutoff scores are calculated by BLAST^® algorithms and cannot be changed.

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BLAST^® reference information provided in whole or in part from the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health.