note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
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Introduction to similarity searching<br />
Similarity Searching with GETSIM<br />
Protein sequence search example<br />
Search Question: To find peptide sequences which have similarity to the following<br />
sequence:<br />
Page 32 | GENESEQ on STN (DGENE) Workshop Manual<br />
CKSTLGRNCYNLCRARGAQKLCANVCRCKLTSGLSCPKDFP<br />
Search Strategy<br />
To conduct a GETSIM similarity search for protein sequences …<br />
Step 1 Conduct a GETSIM search and select answers<br />
Step 2 Sort the answer set by descending similarity score<br />
Step 3 Display using a free-of-charge format with alignment<br />
Step 4 Display selected answers in a bibliographic format<br />
RUN GETSIM for a SQP search<br />
=> FILE DGENE<br />
FILE 'DGENE' ENTERED AT 16:05:47 ON 28 DEC 2010<br />
COPYRIGHT (C) 2010 THOMSON REUTERS<br />
=> RUN GETSIM CKSTLGRNCYNLCRARGAQKLCANVCRCKLTSGLSCPKDFP/SQP<br />
RUN GETSIM AT 16:05:49 ON 28 DEC 2010<br />
COPYRIGHT (C) 2010 <strong>FIZ</strong> KARLSRUHE GMBH<br />
160000 SEQUENCES PROCESSED<br />
350000 SEQUENCES PROCESSED<br />
. . . .<br />
6200000 SEQUENCES PROCESSED<br />
6490000 SEQUENCES PROCESSED<br />
Sequence queries can be entered<br />
directly on the command line, or<br />
sent as a plain text file via the<br />
Query Upload Wizard (page 14).<br />
(continued on next page)
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