note - FIZ Karlsruhe

Introduction to similarity searching
Expectation value (-E)
Expectation value (E-Value) is the statistical significance threshold for reporting matches against a
sequence database. The E-value can be any positive number, and the default value is 10. This
means that 10 matches may be expected to be found merely by chance. In general, the E-value is
lowered to make the search more precise and raised to retrieve more answers.
Peptide similarity matrices (-M)
For peptide-based searches SQP and TSQN, the advanced options provide additional scoring
matrices to the default BLOSUM-62. Guidelines from the NCBI, regarding the use of scoring
matrices for peptide queries of various lengths, are shown in the table below.
Query Length Matrix Gap costs
85 BLOSUM-62 (11,1) (BLAST default)
Decide how many answers to keep
After the BLAST or GETSIM search is completed a candidate answer set consisting of sequences
exceeding a certain similarity threshold 1 is collated. A diagram is generated that shows the scores
of the retrieved sequences. The x-axis represents the number of sequence record answers with a
specific similarity score, and the y-axis is scaled by the corresponding similarity scores. Also
provided above the diagram are the Query Self Score – which is the similarity score of the query
mapped against itself – and the score of the best answer retrieved in the results set.
After assessing the display of the diagram, the whole candidate answer set, a subset of the answer
set, or a subset represented by a minimum percentage of the Query Self Score may be kept. If
only a subset is required, this is specified by answering "How many answers would you like to
keep?" with the either the number of desired records, or the appropriate minimum percentage of
the Query Self Score, followed by the percent sign (%). The candidate answer set may contain up
to 10,000 best scoring candidate sequences.
Sort answers by similarity score
The answer set L-number generated after the search (above), contains sequence records sorted by
descending database entry date. BLAST and GETSIM sequence records may resorted into
descending score order. Just type SOR SCORE D at the arrow prompt. Alternatively, BLAST
search results may be resorted into BLAST identity percentage order, using SOR IDENT D.
Example
=> SOR SCORE D
PROCESSING COMPLETED FOR L2
L3 153 SOR L2 SCORE D
1 For BLAST searches the threshold is defined by the “expectation value”. For GETSIM searches the threshold is an
automatically adjusted function of the query length, query type and database size.
Page 16 | GENESEQ on STN (DGENE) Workshop Manual