note - FIZ Karlsruhe

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