note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
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Introduction to similarity searching<br />
Check if the sequence was uploaded correctly with D LQUE<br />
=> D L1 LQUE<br />
L1 ANSWER 1 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN<br />
LQUE MSSFKWCFTLNYSSAAEREDFLALLKEEELNYAVVGDEVAPSSGQKHLQGYLSLKKSIKLGGLKKKYSSRAHW<br />
ERARGSDEDNAKYCSKETLILELGFPASQGSNRRKLSEMVSRSPERMRIEQPEIYHRYTSVKKLKKFKEEFVH<br />
PCLDRPWQIQLTEAIDEEPDDRSIIWVYGPNGNEGKSTYAKSLMKKDWFYTRGGKKENILFSYVDEGSEKHIV<br />
FDIPRCNQDYLNYDVIEALKDRVIESTKYKPIKLVELINIHVIVMANFMPEFCKISEDRIKIIYC<br />
Conduct a BLAST search in SQP mode and keep all answers<br />
=> RUN BLAST L1 /SQP<br />
BLAST Version 2.2<br />
BLAST version and<br />
literature references<br />
The BLAST software is used herein with permission of the National are indicated Center before for<br />
Biotechnology Information (NCBI) of the National Library of Medicine<br />
each BLAST search.<br />
(NLM).<br />
. . . .<br />
45 ANSWERS FOUND BELOW EXPECTATION VALUE OF 10.0<br />
QUERY SELF SCORE VALUE IS 510<br />
BEST ANSWER SCORE VALUE IS 457<br />
Similarity<br />
The Best Answer Score value is also<br />
Score<br />
given. In this example, there is no<br />
457 ||<br />
perfect answer match for the query.<br />
||<br />
||<br />
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The graphic representation gives a count<br />
||||<br />
of hit sequences (x-axis) and similarity<br />
229 ||||<br />
score (y-axis). The graph gives a visual<br />
||||<br />
clue about the proportion of similar and<br />
||||<br />
not so similar sequences in the answer set.<br />
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Answer Count 10 20 30 40 50<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 89%)<br />
ENTER (ALL) OR ? :ALL<br />
L2 RUN STATEMENT CREATED<br />
L2 45 MSSFKWCFTLNYSSAAEREDFLALLKEEELNYAVVGDEVAPSSGQKHLQG<br />
YLSLKKSIKLGGLKKKYSSRAHWERARGSDEDNAKYCSKETLILELGFPA<br />
SQGSNRRKLSEMVSRSPERMRIEQPEIYHRYTSVKKLKKFKEEFVHPCLD<br />
RPWQIQLTEAIDEEPDDRSIIWVYGPNGNEGKSTYAKSLMKKDWFYTRGG<br />
KKENILFSYVDEGSEKHIVFDIPRCNQDYLNYDVIEALKDRVIESTKYKP<br />
IKLVELINIHVIVMANFMPEFCKISEDRIKIIYC/SQP. -E 10.0<br />
Page 22 | GENESEQ on STN (DGENE) Workshop Manual<br />
The Query Self Score value is the ideal<br />
score for a perfect answer match.<br />
In this example, ALL answers are kept (L2).
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