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Search Statistics in Result Report

This is an example of the statistical details that are appended to a CAS RegistrySM 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:

  1. Dropoff for the ungapped extension (the HSP).
  2. Dropoff parameter used in the first gapped extension.
  3. 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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