note - FIZ Karlsruhe

9590 ANSWERS FOUND ABOVE A THRESHOLD OF 58
QUERY SELF SCORE VALUE IS 309
BEST ANSWER SCORE VALUE IS 309
Introduction to similarity searching
Similarity
The Best Answer Score value is also
Score
given. In this example, there is at least
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one perfect answer match to the query.
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The graphic representation gives a count
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of hit sequences (x-axis) and similarity
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score (y-axis). The graph gives a visual
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clue about the proportion of similar and
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not so similar sequences in the answer set.
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Answer Count 1920 3840 5760 7680 9600
ENTER EITHER THE NUMBER OF ANSWERS YOU WISH TO KEEP
OR ENTER MINIMUM PERCENT OF SELF SCORE FOLLOWED BY %
(BEST ANSWER PERCENTAGE OF SELF SCORE IS 100%)
ENTER (ALL) OR ? :70%
In this example, answers with at least 70% of the
L1 RUN STATEMENT CREATED
Query Self Score are kept. answers are selected (L1).
L1 35 CKSTLGRNCYNLCRARGAQKLCANVCRCKLTSGLSCPKDFP/SQP
Sort similarity score descending
Answer set arranged by accession number; to sort by descending
similarity score, enter at an arrow prompt (=>) "sor score d".
=> SOR SCORE D
PROCESSING COMPLETED FOR L1
L2 35 SOR L1 SCORE D
Helpful
HINT
The Query Self Score value is the ideal
score for a perfect answer match.
GETSIM is slower than BLAST, so using GETSIM in BATCH mode is
recommended. In addition, BATCH query limits are higher. See page 79.
GENESEQ on STN (DGENE) Workshop Manual | Page 33