note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
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Upload the sequence and conduct a BLAST search<br />
=> FILE DGENE<br />
FILE 'DGENE' ENTERED AT 11:53:58 ON 28 DEC 2010<br />
COPYRIGHT (C) 2010 THOMSON REUTERS<br />
Introduction to similarity searching<br />
=> UPL R BLAST<br />
Uploading C:\Documents and Settings\Rob Austin\Desktop\BBTV protein.txt<br />
UPLOAD SUCCESSFULLY COMPLETED<br />
L1 GENERATED<br />
=> RUN BLAST L1 /SQP<br />
BLAST Version 2.2<br />
The BLAST software is used herein with permission of the National Center for<br />
Biotechnology Information (NCBI) of the National Library of Medicine (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 />
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The graphic representation gives a count<br />
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of hit sequences (x-axis) and similarity<br />
229 ||||<br />
score (y-axis). The graph gives a visual<br />
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clue about the proportion of similar and<br />
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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 />
See page 21 for instructions on how to<br />
upload the sequence query text file.<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).<br />
L2 45 MSSFKWCFTLNYSSAAEREDFLALLKEEELNYAVVGDEVAPSSGQKHLQG<br />
YLSLKKSIKLGGLKKKYSSRAHWERARGSDEDNAKYCSKETLILELGFPA<br />
SQGSNRRKLSEMVSRSPERMRIEQPEIYHRYTSVKKLKKFKEEFVHPCLD<br />
RPWQIQLTEAIDEEPDDRSIIWVYGPNGNEGKSTYAKSLMKKDWFYTRGG<br />
KKENILFSYVDEGSEKHIVFDIPRCNQDYLNYDVIEALKDRVIESTKYKP<br />
IKLVELINIHVIVMANFMPEFCKISEDRIKIIYC/SQP. -E 10.0<br />
GENESEQ on STN (DGENE) Workshop Manual | Page 41
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