note - FIZ Karlsruhe

Text and Bibliographic searching
Check if the sequence was uploaded correctly with D LQUE
=> D LQUE
L1 ANSWER 1 DGENE COPYRIGHT 2010 THOMSON REUTERS ON STN
LQUE CGTTGCTCTGGGATTTCTTTGCTGGATTCCAGACTTTTGCTGTCAGGTATTGCTTCTTTACTTTCTCCTTTAT
TAGGTTTTTTTCTTTTCCTCTCCCTTCCTTTTTTTCCTCGTTCTCCCTTCTGACACTTCTTCCTTTGCACTGT
ACACTTTCTTGTCTCATTTGTTGGGGGACATAGGTTACCCTTTGCTGAAGGATGCTGTATTATTTCTCGGACC
CGTGTTTCAGTCCCTCTTTTGAAGCCACATGTTTTTCCCTTCTTCGTGCATGGACTCCAAGGATTCCATTCAC
TGACCTCACAGTGCACAATACTGACACACTCCATAGTATGGTTGTTGGCTTCCAACCCTTCTGGGCAATTGTC
AAGGCACTTTCCAAGGTGTAAGTAN
In this example a BLAST nucleic acid search (/SQN) is run in offline BATCH mode
=> RUN BLAST L1/SQN -F F BATCH
PLEASE ENTER BATCH IDENTIFIER (MAX. 8 CHARS):ESTHIV
TO BE NOTIFIED WHEN THIS BATCH SEARCH IS COMPLETE,
PLEASE ENTER YOUR EMAIL ADDRESS (MAX. 50 CHARS) OR "NONE"
INPUT: OR (END):ROBERT.AUSTIN@FIZ-KARLSRUHE.DE
Enter a valid email address to
BLAST Version 2.2
receive email notification when
the BATCH search is complete.
The BLAST software is used herein with permission of the
National Center for Biotechnology Information (NCBI) of
the National Library of Medicine (NLM). See also, Altschul,
Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui
Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein
database search programs." Nucleic Acids Res. 25:3389-3402
BATCH PROCESSING STARTED FOR ESTHIV
=> LOG H
Tip: use LOGOFF HOLD (LOG H) to be able
to return to an STN session within two hours.
SESSION WILL BE HELD FOR 120 MINUTES
STN INTERNATIONAL SESSION SUSPENDED AT 14:19:03 ON 28 DEC 2010
Log back in to STN to retrieve the BLAST offline BATCH search results
* * * * * * RECONNECTED TO STN INTERNATIONAL * * * * * *
SESSION RESUMED IN FILE 'HOME' AT 15:10:34 ON 28 DEC 2010
FILE 'DGENE' ENTERED AT 15:10:34 ON 28 DEC 2010
=> RUN GETBATCH ESTHIV
Please enter your batch identifier
or enter # for batch id list
or enter * for batch id at top of list
or enter - before batch id to delete
or enter . for (end)
. . . .
Page 94 | GENESEQ on STN (DGENE) Workshop Manual
The sequence query is now ready for searching
directly in DGENE using the L-number (L1).
Add BATCH to the end of a
RUN BLAST command to
search in offline batch
search mode (see page 79).
Use the RUN GETBATCH to
retrieve the BLAST search
results (see page 79).
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