note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
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Advanced similarity searching<br />
Translated protein similarity search<br />
GETSIM translated protein (/TSQN) similarity search<br />
When <strong>FIZ</strong> <strong>Karlsruhe</strong> receives GENESEQ data from Thomson Reuters all the nucleic acid<br />
sequences are automatically translated into protein sequences, according to the Universal Genetic<br />
Code (page 127). These translated protein sequences are loaded into a behind-the-scenes database<br />
which is then used as an intermediate step between a protein TSQN search query and nucleic acid<br />
sequence records in DGENE. Both the SIN and COM strands (page 48) are translated using all<br />
three reading frames. Thus a single protein query will be searched against all six possible<br />
translations, from the three reading frames of both the SIN and COM nucleic acid sequences.<br />
Search Question: Find nucleic acid sequences which have translated similarity to the<br />
following protein sequence query:<br />
Helpful<br />
HINT<br />
GQIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSY<br />
DFHQLKKFLKIALETPARICPINYSLLASLLPKGYPGRVN<br />
EILHILIQTQ<br />
Search Strategy<br />
To conduct a translated similarity search for a protein sequence<br />
using GETSIM TSQN. . .<br />
Step 1 RUN GETSIM using the translated (/TSQN) option<br />
Step 2 Sort the results by Smith-Waterman score<br />
Step 3 Display using a free of charge format with alignment<br />
Step 4 Display selected answers in a bibliographic format<br />
See also the BLAST TSQN search example given in the USGENE Workshop<br />
Manual (page 102): http://www.stn-international.com/usgene_wm.html.<br />
Page 74 | GENESEQ on STN (DGENE) Workshop Manual
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