note - FIZ Karlsruhe

Upload the sequence query text file via the STN Express Upload Query Wizard
=> FILE DGENE
FILE 'DGENE' ENTERED AT 18:00:28 ON 28 DEC 2010
COPYRIGHT (C) 2010 THOMSON REUTERS
Advanced similarity searching
=> UPL R BLAST
Uploading C:\Documents and Settings\Rob Austin\Desktop\IL1RN_MRNA.txt
UPLOAD SUCCESSFULLY COMPLETED
L1 GENERATED
Verify the uploaded sequence with D LQUE
=> D LQUE
L1 ANSWER 1 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN
LQUE GGAAGAGACCCTGCAAGATGCAAGCCTTCAGAATCTGGGATGTTAACCAGAAGACCTTCTACATGAGGAATAA
CCAACTAGTTGCTGGATACTTGCAAGAATCAAATACTAAATTACAAGAGAAGATAGATGTGGTGCCCATTGAG
CCTGATGCTCTATTCCTGGGACTCCATGGGAGGAAGCTGTGCCTGGCCTGTGTCAAGTCTGGTGATGAGATTA
GGTTCCAATTGGAGGCAGTTAACATCACTGA
RUN the BLAST /SQN (BLASTN) search and decide how many answers to keep
=> RUN BLAST L1 /SQN –F F
BLAST Version 2.2
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
BLAST SEARCHING
. . . .
These commands are automatically run by the
STN Express Query Upload wizard (page 21).
The sequence query is now ready for searching
directly in DGENE using the L-number (L1).
Turn the Low Complexity Filter off
with the syntax: /SQP –F F.
BLAST version and
literature references
are indicated before
each BLAST search.
394 ANSWERS FOUND BELOW EXPECTATION VALUE OF The 10.0 Query Self Score value is the ideal
score for a perfect answer match.
QUERY SELF SCORE VALUE IS 496
BEST ANSWER SCORE VALUE IS 496
The Best Answer Score value is also
given. In this example, there is at least
one perfect answer match.
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GENESEQ on STN (DGENE) Workshop Manual | Page 69