note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
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Current Awareness Alert Searching<br />
Advanced similarity searching<br />
Both RUN GETSIM and RUN BLAST have an automatic ALERT feature for current awareness<br />
similarity searching. The automatic alert is run routinely against updates of the database, i.e.<br />
every two weeks. Results must be collected online, and at any time up to three months from the<br />
Alert run. Up to sixteen simultaneous Alerts can be running and up to 96 result sets stored per<br />
login ID. Collected ALERT result sets will remain available until the next update (unless they<br />
have already been deleted by the searcher).<br />
There is no charge for initiating and executing an Alert, but the result sets will be subject to a<br />
charge on collection. Uncollected or incomplete (GETSIM) answer sets will not be charged for.<br />
Empty answer sets from ALERT are clearly marked in the output queue.<br />
<strong>note</strong><br />
The score threshold for GETSIM similarity searches has been lowered for<br />
ALERT compared to the standard procedure (against the whole database).<br />
This reflects the smaller number of sequences being searched (only one<br />
database update), and also has the benefit of higher sensitivity.<br />
To initiate a current awareness similarity search, add ALERT to the end the RUN GETSIM or<br />
RUN BLAST command. The system will then prompt you for a batch request identifier (name)<br />
which can consist of up to 8 letters or numbers, e.g. PROTEIN1. Use RUN ALERT to review the<br />
status of ALERT searches and retrieve results.<br />
Initiation of ALERT searches:<br />
=> RUN GETSIM L1 /SQN BOTH ALERT<br />
PLEASE ENTER ALERT IDENTIFIER (MAX. 8 CHARS):AQUAP1<br />
PLEASE ENTER ALERT TITLE (MAX. 40 CHARS):AQUAPORINNG<br />
. . . .<br />
NEW ALERT CREATED<br />
Entering a second ALERT<br />
=> RUN BLAST L1 /SQN ALERT<br />
PLEASE ENTER ALERT IDENTIFIER (MAX. 8 CHARS):AQUAP2<br />
PLEASE ENTER ALERT TITLE (MAX. 40 CHARS):AQUAPORINNB<br />
BLAST Version 2.2<br />
. . . .<br />
NEW ALERT CREATED<br />
GENESEQ on STN (DGENE) Workshop Manual | Page 83