note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
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Sequence Code Match Searching<br />
Background<br />
Complementary Nucleic Acid Searching<br />
Unlike a nucleic acid BLAST search (page 12), a RUN GETSEQ search does NOT automatically<br />
search both a nucleic acid query and its complementary sequence. To retrieve complementary<br />
answers of interest the appropriate sequence must be derived 1 and searched as a separate query.<br />
<strong>note</strong><br />
Remember that by convention all nucleic acid sequences in DGENE are<br />
read/written from 5' (left) to 3' (right). So it is necessary to generate and<br />
search the reverse complement 1 sequence from the original query.<br />
Search Question: Find sequences which match the complementary version of the<br />
following sequence: GAGCTCGAATT<br />
Search Strategy<br />
To find complementary nucleic acid sequences in DGENE…<br />
Step1<br />
Step2<br />
Step3<br />
Try the EXACT sequence search<br />
Derive the complementary sequence<br />
Run the complementary search<br />
Run the exact nucleic acid sequence search<br />
=> RUN GETSEQ GAGCTCGAATT/SQEN<br />
RUN GETSEQ AT 18:40:52 ON 30 DEC 2010<br />
COPYRIGHT (C) 2010 <strong>FIZ</strong> KARLSRUHE GMBH<br />
GETSEQ CONTINUING...<br />
L1 RUN STATEMENT CREATED<br />
L1 0 GAGCTCGAATT/SQEN<br />
1 For example, using a Reverse Complement tool: http://www.bioinformatics.org/sms/rev_comp.html<br />
Page 120 | GENESEQ on STN (DGENE) Workshop Manual
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