note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
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Protein SUBSEQUENCE FAMILY Search<br />
Sequence Code Match Searching<br />
SUBSEQUENCE search results can also be enhanced using the family equivalence approach, by<br />
introducing conservative substitution in the amino acid sequence. The amino acid chemical<br />
families used for this substitution are shown in the table on page 103.<br />
Search Question: Find all patent references for the following polypeptide fragment:<br />
SAILRTLFRCRNEKKKHRAV<br />
Search Strategy<br />
To find protein family subsequence answers DGENE…<br />
Step 1 Try the SUBSEQUENCE search<br />
Step 2<br />
Step 3<br />
Subsequence search<br />
Run the SUBSEQUENCE family search<br />
=> RUN GETSEQ SAILRTLFRCRNEKKKHRAV/SQSP<br />
RUN GETSEQ AT 18:03:58 ON 30 DEC 2010<br />
COPYRIGHT (C) 2010 <strong>FIZ</strong> KARLSRUHE GMBH<br />
Display the sequence and patent information<br />
L1 RUN STATEMENT CREATED<br />
L1 1 SAILRTLFRCRNEKKKHRAV/SQSP<br />
Subsequence family search<br />
=> RUN GETSEQ SAILRTLFRCRNEKKKHRAV/SQSFP<br />
RUN GETSEQ AT 18:04:42 ON 30 DEC 2010<br />
COPYRIGHT (C) 2010 <strong>FIZ</strong> KARLSRUHE GMBH<br />
L2 RUN STATEMENT CREATED<br />
L2 8 SAILRTLFRCRNEKKKHRAV/SQSFP<br />
=> S L2 NOT L1<br />
L3 7 L2 NOT L1<br />
One answer is found (L1) using SQSP.<br />
Seven additional answers are found<br />
(L3) using SQSFP.<br />
GENESEQ on STN (DGENE) Workshop Manual | Page 111
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