note - FIZ Karlsruhe

Introduction to similarity searching
Sort similarity score descending
=> SOR SCORE D
PROCESSING COMPLETED FOR L2
L3 8554 SOR L2 SCORE D
Display the results using ALIGN and SCORE
=> D TRIAL SCORE ALIGN 1,500,8554
L3 ANSWER 1 OF 8554 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN
AN AEF76660 DNA DGENE
TI Isolated nucleic acid, coded for a fusion protein, is formed by two
functionally bonded nucleic acid sequences where one is derived from a
mycovirus.
DESC Human herpesvirus 5 pp65 encoding DNA SEQ ID NO 1.
KW recombinant protein; fusion protein; therapeutic; infectious disease;
protein expression; vaccine; protein engineering; enzyme engineering; ds;
gene.
SQL 3426
SCORE 251 96% of query self score 260
ALIGN Smith-Waterman score: 251
The ALIGN display:
52 na overlap starting at 2631
� First line: portion of query with similarity
ggguuuaggagugguaggucuuacgaugccagcuguaaugccuaccggataa
:::...:::::.::.:::.:..::::.::::::.:.::.:::.:::::: � Second line: similarity :: (2 dots-identical
gggtttaggagtggtaggtcttacgatgccagctgtaatgcctaccggagaa
residues, blank-no match)
� Third line: portion of retrieved sequence
L3 ANSWER 500 OF 8554 DGENE COPYRIGHT 2010 with THOMSON similarityREUTERS
on STN
AN ATE39398 cDNA DGENE
TI New substantially purified expressed sequence tags (ESTs) isolated from
cotton, useful for reducing or increasing expression of a protein in a
plant cell and as a unique molecular tool for the targeting and isolation
of novel genes.
DESC Cotton expressed sequence tag SEQ ID NO 36640.
KW stress tolerance; EST; expressed sequence tag; gene expression;
transgenic plant; plant breeding; crop improvement; mapping; ss.
SQL 576
SCORE 86 33% of query self score 260
ALIGN Smith-Waterman score: 86
28 na overlap starting at 321 (229 in complement)
agugguaggucuuacgaugccagcugua
: .::. :: ..:::: :::::: :.:
actggtgggcgttacgaagccagcggta
“In complement” means that the hit sequence was
found in the complementary (COM) strand. This
answer was retrieved because of using /SQN BOTH.
L3 ANSWER 8554 OF 8554 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN
AN ADN03813 cDNA DGENE
TI New PRO nucleic acid or polypeptide, useful for preparing a
pharmaceutical composition for diagnosing or treating psoriasis in a
mammal.
DESC Antipsoriatic cDNA sequence #105.
KW ds; gene; antipsoriatic; gene therapy; psoriasis; Smith-Waterman diagnosis. score is shown
SQL 5175
as a percentage in the SCORE
SCORE 67 25% of query self score 260 field; 100% is the score of the
ALIGN Smith-Waterman score: 67
query against itself.
44 na overlap starting at 1948
uuuaggagugguaggucuuacgaugccagcuguaaugccuaccg
... ::: : .: :::: :::: . : .::: ::::
ttttggacagatatcatcaacgaagccattttcagtgccaaccg
Page 38 | GENESEQ on STN (DGENE) Workshop Manual