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 ATGCCAACAGATCACGAGCAGCCCTGTGGTCCCAGGCACAGGTCATTTTGCCTCAATGGGGGGATTTGTTATG<br />
TGATCCCTACTATCCCCAGCCCATTCTGTAGGTGCATTGAAAATTACACCGGAGCACGCTGCGAAGAGGTTTT<br />
TCTCCCAAGCTCCAGCATCCCAAGCGAAAGTAATCTGTCGGCAGCTTTCGTGGTGCTGGCGGTCCTCCTCACT<br />
CTTACCATCGCGGCGCTCTGCTTCCTGTGCAGGAAGGGCCACCTTCAGAGGGCCAGTTCAGTCCAGTGTGAGA<br />
TCAGCCTGGTAGAGACAAACAATACCAGAACCCGTCACAGCCACAGAGAACACTGA<br />
Conduct a BLAST search in SQN mode and keep all answers<br />
=> RUN BLAST L1 /SQN<br />
BLAST version and<br />
BLAST Version 2.2<br />
literature references<br />
are indicated before<br />
The BLAST software is used herein with permission of the National each BLAST Center search. for<br />
Biotechnology Information (NCBI) . . . .<br />
58 ANSWERS FOUND BELOW EXPECTATION VALUE OF 10.0<br />
QUERY SELF SCORE VALUE IS 690<br />
BEST ANSWER SCORE VALUE IS 690<br />
Similarity<br />
The Best Answer Score value is also<br />
Score<br />
given. In this example, there is at least<br />
690 |<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 />
345 ||<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 20 40 60 80 100<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 ? :ALL<br />
L2 RUN STATEMENT CREATED<br />
L2 58 ATGCCAACAGATCACGAGCAGCCCTGTGGTCCCAGGCACAGGTCATTTTGCCTCAATGGGG<br />
GGATTTGTTATGTGATCCCTACTATCCCCAGCCCATTCTGTAGGTGCATTGAAAATTACAC<br />
CGGAGCACGCTGCGAAGAGGTTTTTCTCCCAAGCTCCAGCATCCCAAGCGAAAGTAATCTG<br />
TCGGCAGCTTTCGTGGTGCTGGCGGTCCTCCTCACTCTTACCATCGCGGCGCTCTGCTTCC<br />
TGTGCAGGAAGGGCCACCTTCAGAGGGCCAGTTCAGTCCAGTGTGAGATCAGCCTGGTAGA<br />
GACAAACAATACCAGAACCCGTCACAGCCACAGAGAACACTGA/SQN. -E 10.0<br />
Page 28 | 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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