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