note - FIZ Karlsruhe

RUN GETSIM for a SQN BOTH search
Introduction to similarity searching
=> FILE DGENE
Sequence queries can be entered directly on
FILE 'DGENE' ENTERED AT 13:06:43 ON 28 DEC 2010 the command line, or sent as a plain text file
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via the Query Upload Wizard (page 14).
=> RUN GETSIM GGGUUUAGGAGUGGUAGGUCUUACGAUGCCAGCUGUAAUGCCUACCGGATAA/SQN BOTH
RUN GETSIM AT 13:07:03 ON 28 DEC 2010
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. . . .
8725 ANSWERS FOUND ABOVE A THRESHOLD OF 67
QUERY SELF SCORE VALUE IS 260
BEST ANSWER SCORE VALUE IS 260
Similarity
The Best Answer Score value is also
Score
given. In this example, there is at least
260 |
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 1750 3500 5250 7000 8750
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 ? :ALL In this example, ALL are answers kept (L1).
L1 RUN STATEMENT CREATED
L1 8722 GGGUUUAGGAGUGGUAGGUCUUACGAUGCCAGCUGUAAUGCCUACCGGATAA/SQN.BOTH
Answer set arranged by accession number; to sort by descending
similarity score, enter at an arrow prompt (=>) "sor score d".
Further refinement with sequence length
=> S L1 AND SQL>100
13125023 SQL>100
L2 8554 L1 AND SQL>100
The Query Self Score value is the ideal
score for a perfect answer match.
For this example we are not interested in
sequences under 101 nucleotides. This is
accomplished by making use of the sequence
length field, i.e. SQL>100.
GENESEQ on STN (DGENE) Workshop Manual | Page 37