note - FIZ Karlsruhe

Advanced similarity searching
Display the results using ALIGN and SCORE
=> D TRIAL SCORE ALIGN 1-46
L2 ANSWER 1 OF 46 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN
AN AEN13227 DNA DGENE
TI Purified nucleic acid hybridizing with genomic RNA, for diagnostic
methods, kits, vaccines, or antiviral therapy, is obtained from human T-
cell lymphotropic virus.
DESC HTLV-3 genomic sequence, SEQ ID NO:68.
KW immunoassay; antibody; hybridization; diagnostic; Smith-Waterman microorganism score for TSQN is
detection; therapeutic; vaccine; coding sequence; the similarity ds. between the query and
SQL 9078
the retrieved translated polypeptide
SCORE 615 100% of query self score 615 sequence.
ALIGN Smith-Waterman score: 615
90 aa overlap starting at 316 (Frame 2 - 270 na overlap starting at 947)
gqifsrsaspiprpprglaahhwlnflqaayrlepgpssydfhqlkkflkialetparic
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
The TSQN ALIGN display is similar to SQP:
gqifsrsaspiprpprglaahhwlnflqaayrlepgpssydfhqlkkflkialetparic
� First line: portion of the query with similarity
pinysllasllpkgypgrvneilhiliqtq
� Second line: similarity (2 dots-identical
::::::::::::::::::::::::::::::
residues, 1 dot family match, blank-no match)
pinysllasllpkgypgrvneilhiliqtq
� Third line: portion of the retrieved translated
L2 ANSWER 2 OF 46 DGENE COPYRIGHT 2010 THOMSON polypeptide REUTERS sequence on with STN similarity
AN AEN13229 DNA DGENE
TI Purified nucleic acid hybridizing with genomic RNA, for diagnostic
methods, kits, vaccines, or antiviral therapy, is obtained from human T-
cell lymphotropic virus.
DESC HTLV-3 genomic sequence, SEQ ID NO:70.
KW immunoassay; antibody; hybridization; diagnostic; microorganism
detection; therapeutic; vaccine; coding sequence; ds.
SQL 8393
SCORE 615 100% of query self score 615
ALIGN Smith-Waterman score: 615
90 aa overlap starting at 266 (Frame 1 - 270 na overlap starting at 796)
gqifsrsaspiprpprglaahhwlnflqaayrlepgpssydfhqlkkflkialetparic
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
gqifsrsaspiprpprglaahhwlnflqaayrlepgpssydfhqlkkflkialetparic
Before pinysllasllpkgypgrvneilhiliqtq
parentheses: The overlap of the
In parentheses: The region of the nucleic
polypeptide ::::::::::::::::::::::::::::::
query sequence to the
acid sequence (SEQ) which relates to the
retrieved pinysllasllpkgypgrvneilhiliqtq
translated polypeptide sequence. retrieved translated polypeptide sequence.
L2 ANSWER 3 OF 46 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN
AN AAT42902 DNA DGENE
TI DNA molecule with gene expression regulation activity - for use in e.g.
treatment of human T-cell leukaemia and HIV, as antivirus agent and for
detecting cancer
DESC DNA sequence which regulates expression in HTLV and HIV.
KW gene expression; regulation; plasmid; viral infection; human T-cell
leukaemia; HIV; antivirus agent; detection; cancer; gene therapy; TSP;
ss.
SQL 9045
SCORE 615 100% of query self score 615
ALIGN Smith-Waterman score: 615
90 aa overlap starting at 269 (Frame 1 - 270 na overlap starting at 805)
gqifsrsaspiprpprglaahhwlnflqaayrlepgpssydfhqlkkflkialetparic
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
gqifsrsaspiprpprglaahhwlnflqaayrlepgpssydfhqlkkflkialetparic
pinysllasllpkgypgrvneilhiliqtq
::::::::::::::::::::::::::::::
pinysllasllpkgypgrvneilhiliqtq
Page 76 | GENESEQ on STN (DGENE) Workshop Manual