Searching for siRNA and miRNA in STN® patent ... - STN International

Searching for siRNA and miRNA 

in STN ® patent databases 

Robert Austin – FIZ Karlsruhe

Agenda 

• Introduction to RNAi, miRNA and siRNA 

• Understanding siRNA and miRNA indexing in 

DGENE, DWPISM , REGISTRY, and CAplusSM • Sequence searching using DGENE, USGENE ® , 

PCTGEN and REGISTRY 

– Sequence Code Match (SCM) and GETSIM 

– Multi-file BLAST search and post-processing 

See also: Sequence Basics e-Seminar (July 2012): 

http://www.stn-international.com/Sequence_Basics_Seminar.html 

2

Why use STN sequence databases? 

• Sequence information on STN is comprehensive 

– Four sequence databases allow users to achieve a 

comprehensive search of sequences from both patent 

and non-patent documents 

• Sequence databases on STN are timely 

– Allows you to keep up-to-date with the most current 

information 

• Sequence indexing is unique 

– Allows you to retrieve sequences containing 

uncommon residues or chemical modifications that 

are difficult to find 

3

STN sequence searchable databases 

• DGENE 

– Thomson Reuters GENESEQ TM 

– Value-added patent sequence data from around the globe 

• USGENE 

– The USPTO Genetic Sequence Database 

– All available sequence data from the USPTO 

• PCTGEN 

– WIPO/PCT Patent Application Biosequences 

– All available e-published sequence data from WIPO 

• CAS REGISTRY SM 

– Chemical Abstracts Service (CAS) REGISTRY 

– Worldwide value-added patent and non-patent sequences 

4

RNA interference (RNAi) is a mechanism 

that inhibits translation of targeted mRNA 

• 2006 Nobel Prize 

– Andrew Z. Fire 

• Stanford University, California 

– Craig C. Mello 

• University of Massachusetts Medical School in 

Worcester 

– Double-stranded RNA triggers suppression of gene 

activity in a homology-dependent manner, a process 

named RNA interference (RNAi) 

5

RNAi pathway 

miRNA 

RISC 

RISC 

siRNA complexes 

with RISC 

RISC 

Dicer 

dsRNA 

siRNA 

The antisense siRNA (guide 

strand) within RISC binds 

complementary to the mRNA 

Diagram Key: 

Dicer = an enzyme that cleaves double stranded RNA 

dsRNA = double stranded RNA 

mRNA = messenger RNA 

miRNA = micro RNA 

RISC = RNA‐induced silencing complex 

siRNA = short interfering RNA 

The cleaved mRNA 

undergoes degradation 

RISC 

Cleaved 

mRNA 

An enzyme within 

RISC cleaves the 

mRNA 

mRNA 

6

Two types of RNA seen in RNAi 

• Short interfering RNA (siRNA) 

– Also known as small interfering RNA or silencing RNA 

– siRNAs are double-stranded (ds) and originate from 

perfectly base-paired dsRNA precursors 

– Short 19-25 nucleotides (typically, 21) 

• Micro RNA (miRNA) 

– miRNAs are single-stranded (ss) and originate from 

imperfectly base-paired hairpin structure transcripts 

– Short 19-23 nucleotides (typically, 22) 

• Both play a role in the RNAi pathway 

– Interfere with the expression of a specific gene 

7

http://en.wikipedia.org/wiki/Small_interfering_RNA 

siRNA sequence structure 

8

miRNA sequence structure 

Example from miRBase: 

www.mirbase.org. 

9

Applications of RNAi and siRNA 

• Functional studies of genes 

– Decrease gene expression (gene knockdown) 

– Design genome-wide RNAi libraries for RNAi screening 

• Human disease therapy 

– Possible reversal of induced liver failure in mouse models 

– Treat infection by herpes simplex virus type 2 

– Inhibition of viral gene expression in cancerous cells 

– Potential treatments for neurodegenerative diseases 

• Biotechnology uses 

– Engineering plants that produce lower levels of natural 

plant toxins 

• Diagnosis using miRNA-profiles 

– Indicative of disease states, e.g. heart disease, cancers 

10

Effective RNAi and siRNA therapy 

• RNAi and siRNA target specificity 

– Depends on the position and the sequence 

• The sequence length of RNAi and siRNA 

• The effectiveness of RNAi and siRNA within a 

cell before degradation 

• Delivery method of RNAi and siRNA 

11

Agenda 



DGENE, DWPI, REGISTRY, and CAplus 

• Sequence searching using DGENE, USGENE, 




12

siRNA and miRNA in sequence databases 

• DGENE 

– A clear description (/DESC) is provided, e.g. “Human 

APOC3 gene targeted siRNA antisense strand” 

– Keywords (/KW) are provided: “Micro RNA”, “miRNA”, 

“short interfering RNA”, “siRNA”; others may include “RNA 

interference”, “gene silencing”, and/or “DNA-RNA hybrid” 

– siRNA are indexed as single sequences; ds or ss is 

indexed in the keyword (/KW) field as appropriate 

• REGISTRY 

– The index name (/CN) may include “miRNA”, “siRNA”, etc 

– A description is provided as CAplus linked term text 

– siRNA may be registered either in single stranded or 

double (multi-) stranded RNA records 

13

Example: siRNA patent sequence 

5’-UGCUUAAAAGGGACAGUAUUC-3’ 

3’-CAACGAAUUUUCCCUGUCAUA-5’ 

WO2010083615. 

14

Example: siRNA in DGENE 

L1 ANSWER 1 OF 1 DGENE COPYRIGHT 2012 THOMSON REUTERS on STN 

AN AYE62425 RNA DGENE 

TI Composition useful for treating atherosclerosis, hypertriglyceridemia 

and hypercholesterolemia, comprises small interfering RNA that 

silences apolipoprotein C-III gene expression. 

IN Lee A C H; Macdonald M; Maclachlan I 

PA (PROT-N) PROTIVA BIOTHERAPEUTICS INC. 

PI WO 2010083615 A1 20100729 159 

AI WO 2010-CA120 20100126 

PRAI US 2009-147235P 20090126 

US 2010-293452P 20100108 

PSL Claim 9; Page 130 

DED 16 SEP 2010 (first entry) 

DT Patent 

LA English 

OS 2010-J73486 [50] 

DESC Human APOC3 gene targeted siRNA antisense strand #532. 

ALL format. 

This record is for the siRNA antisense 

strand. There is a separate record in 

DGENE for the sense strand. 

KW APOC3 gene; Apolipoprotein C3; anorectic; antiarteriosclerotic; 

antidiabetic; antiinflammatory; antilipemic; atherosclerosis; 

cardiant; cardiovascular disease; cardiovascular-gen.; coronary 

artery disease; diabetes mellitus; drug delivery; gastrointestinalgen.; 

gene silencing; hypercholesterolemia; hypertriglyceridemia; 

lipid metabolism disorder; metabolic-gen.; nutrition-disorder-gen.; 

obesity; pancreatitis; prophylactic to disease; rna interference; 

short interfering RNA; siRNA; ss; steatosis; therapeutic; vasotropic. 

15

Example: siRNA in DGENE (cont.) 

ORGN Homo sapiens. 

AB The present invention provides a novel composition comprising ALL format a (cont.) 

small 

interfering RNA (siRNA) that silences apolipoprotein C-III (APOC3) 

gene expression useful for treating atherosclerosis, 

hypertriglyceridemia and hypercholesterolemia. The present invention 

also provides methods of delivering and/or administering the lipid 

particles for the treatment of lipid diseases or disorders. The 

present invention independently claims: a nucleic acid-lipid particle 

comprising siRNA, cationic lipid and non-cationic lipid; and a method 

for introducing siRNA that silences APOC3 gene expression into cell. 

The composition and nucleic acid-lipid particle of the present 

invention are useful for preventing, treating, ameliorating and/or 

delaying the onset of atherosclerosis or dyslipidemia (such as 

hypertriglyceridemia and hypercholesterolemia), The DGENE abstract coronary concludes heart with a 

disease, coronary artery disease, fatty liver disease, pancreatitis, 

sentence placing the siRNA sequence 

diabetes, obesity and cardiovascular disease in humans. The 

composition and nucleic acid-lipid in the particle context of the overall present invention. invention 

are so beneficial as they have high solubility, bioavailability, 

biological half-life, and shelf life. The present sequence is a human 

APOC3 gene targeted siRNA antisense strand, which silences the 

apolipoprotein C-III (APOC3) gene expression and is useful in a 

method for treating atherosclerosis, hypertriglyceridemia and 

hypercholesterolemia as described in the present invention. 

NA 6 A; 6 C; 2 G; 0 T; 7 U; 0 Other 

SQL 21 

SEQ 

1 auacuguccc uuuuaagcaa c 

16

Example: siRNA in REGISTRY 

L1 ANSWER 1 OF 1 REGISTRY COPYRIGHT 2012 ACS on STN 

RN 1237573-07-7 REGISTRY 

CN RNA, (A-U-A-C-U-G-U-C-C-C-U-U-U-U-A-A-G-C-A-A-C), complex with RNA 

(U-G-C-U-U-A-A-A-A-G-G-G-A-C-A-G-U-A-U-U-C) (1:1) (CA INDEX NAME) 

OTHER NAMES: 

CN 843: PN: WO2010083615 TABLE: 10 claimed RNA 

FS NUCLEIC ACID SEQUENCE 

SQL 42,21,21 

NA 13 a 9 c 7 g 13 u 

NTE multistranded (2) 

PATENT ANNOTATIONS (PNTE): 

Sequence |Patent 

Source |Reference 

=========+============= 

Not Given|WO2010083615 

|claimed TABLE 

|10 

SEQ 1 auacuguccc uuuuaagcaa c 

SEQ 1 ugcuuaaaag ggacaguauu c 

MF Unspecified 

CI MAN 

SR CA 

LC STN Files: CA, CAPLUS, TOXCENTER 

. . . . 

SQIDE format. 

In REGISTRY, siRNA may be 

indexed as either single or double 

stranded records, depending on 

the applicant/author’s description. 

So, in this example, the 

antisense and sense 

strands are combined into 

a multi-stranded record. 

17

Example: siRNA in CAplus 

L2 ANSWER 1 OF 1 HCAPLUS COPYRIGHT 2012 ACS on STN 

AN 2010:941189 HCAPLUS 

BIB HITIND format. 

DN 153:278052 

TI Small interfering RNA-lipid compositions and methods for silencing 

apolipoprotein C-III expression and treatment of associated disorders 

IN MacDonald, Marcia; Lee, Amy C. H.; MacLachlan, Ian 

PA Protiva Biotherapeutics, Inc., Can. 

. . . . 

FAN.CNT 1 

PATENT NO. KIND DATE APPLICATION NO. DATE 

--------------- ---- -------- -------------------- -------- 

PI WO 2010083615 A1 20100729 WO 2010-CA120 20100126 

. . . . 

IPCI A61K0031-713 [I,A]; A61K0009-14 [I,A]; A61K0009-48 [I,A]; A61P0003-06 

[I,A]; A61P0003-00 [I,C*]; A61P0009-10 The [I,A]; siRNA A61P0009-00 sequence is [I,C*]; linked to 

C12N0015-113 [I,A]; C12N0015-88 [I,A]; C12N0015-87 [I,C*]; C07H0021-02 

Roles and Index Terms in CAplus. 

[I,A]; C07H0021-00 [I,C*]; C07K0014-775 [I,A]; C07K0014-435 [I,C*] 

CC 1-8 (Pharmacology) 

IT 1237559-26-0 1237559-27-1 . . . . 1237573-07-7 1237861-74-3 

1237861-75-4 1237861-76-5 1237861-77-6 1237861-78-7 1237861-79-8 

RL: PRP (Properties); THU (Therapeutic use); BIOL (Biological study); 

USES (Uses) 

(siRNA 2'-OMe modified duplex; siRNA-lipid compns. and methods for 

silencing apolipoprotein C-III expression and treatment of 

associated disorders) 

RE.CNT 4 THERE ARE 4 CITED REFERENCES AVAILABLE FOR THIS RECORD 

ALL CITATIONS AVAILABLE IN THE RE FORMAT 

18

Example: miRNA patent sequence 

WO2009070653. 

Note: this is the miRBase 

example shown on slide 9. 

19

Example: miRNA in DGENE 


AN AWW08667 RNA DGENE 

TRIAL format. 

TI Determining whether a subject has, or is at risk for developing, lung 

cancer associated diseases, comprises measuring the level of microRNA 

(miR) gene product in a peripheral blood sample from the subject. 

DESC Human stem-loop microRNA miR-101-2 used as tumor marker SEQ ID:173. 

KW drug screening; tumor marker; rna detection; rna quantitation; 

prognosis; diagnostic test; prophylactic to disease; therapeutic; 

lung tumor; carcinoma; cytostatic; respiratory tract tumor; 

respiratory-gen.; non-small-cell lung cancer; adenocarcinoma; 

squamous cell carcinoma; dermatological; ss; micro RNA; miRNA; 

microRNA 101-2; MIR101-2. 

SQL 79 

The pre-miRNA gene transcript and/or the 

mature miRNA sequence may be separately 


AN AWW08666 RNA DGENE disclosed and indexed in DGENE. 

TI Determining whether a subject has, or is at risk for developing, lung 

cancer associated diseases, comprises measuring the level of microRNA 

(miR) gene product in a peripheral blood sample from the subject. 

DESC Human mature microRNA miR-101-2 used as tumor marker SEQ ID:172. 

KW drug screening; tumor marker; rna detection; rna quantitation; 

prognosis; diagnostic test; prophylactic to disease; therapeutic; 

lung tumor; carcinoma; cytostatic; respiratory tract tumor; 

respiratory-gen.; non-small-cell lung cancer; adenocarcinoma; 

squamous cell carcinoma; dermatological; ss; micro RNA; miRNA; 

microRNA 101-2; MIR101-2. 

SQL 21 

20

Example: miRNA in REGISTRY 


SQIDE format. 


CN RNA (human microRNA hsa-mir101-2No1 stem-loop sequence)(CA INDEX NAME) 

OTHER NAMES: 

CN 173: PN: WO2009070653 SEQID: 173 claimed RNA 


SQL 79 

NA 20 a 12 c 20 g 27 u 

. . . . 



CN RNA, (U-A-C-A-G-U-A-C-U-G-U-G-A-U-A-A-C-U-G-A-A) (CA INDEX NAME) 

OTHER NAMES: 

CN 172: PN: WO2009070653 SEQID: 172 claimed RNA 


SQL 21 

NA 8 a 3 c 4 g 6 u 

. . . . 

The pre-miRNA gene transcript and/or the 

mature miRNA sequence may be separately 

disclosed and indexed in REGISTRY. 

Note: These SQIDE displays are edited 

to fit on the slide (shown with “….”). 

21

Example: miRNA in CAplus 

L2 ANSWER 1 OF 1 HCAPLUS COPYRIGHT 2012 ACS on STN 

AN 2009:676652 HCAPLUS 

BIB HITIND format. 

DN 151:30960 

TI MicroRNA profiling in peripheral blood in the diagnosis and prognosis 

of lung cancer and in the selection of therapies 

IN Nana-Sinkham, Serge P.; Marsh, Clay B.; Hunter, Melissa G.; . . . . 

PA The Ohio State University Research Foundation, USA 

SO PCT Int. Appl., 102pp. 

CODEN: PIXXD2 

DT Patent 

LA English 

FAN.CNT 1 

PATENT NO. KIND DATE Further APPLICATION descriptive text NO. for the miRNA DATE 

--------------- ---- -------- -------------------- -------- 

sequences is provided as Linked 

Terms in the CAplus Index Terms field. 

PI WO 2009070653 A1 20090604 WO 2008-US84821 20081126 

. . . . 

IT 1159623-39-8 

RL: ANT (Analyte); DGN (Diagnostic use); PRP (Properties); ANST 

(Analytical study); BIOL (Biological study); USES (Uses) 

(nucleotide sequence, microRNA hsa-mir101-2No1; microRNA profiling 

in peripheral blood in diagnosis and prognosis of lung cancer and 

in selection of therapies) 

IT . . . . 1159623-38-7 1159623-40-1 1159623-42-3 1159623-45-6 . . . . 

RL: ANT (Analyte); DGN (Diagnostic use); PRP (Properties); ANST 

(Analytical study); BIOL (Biological study); USES (Uses) 

(nucleotide sequence; microRNA profiling in peripheral blood in 

diagnosis and prognosis of lung cancer and in selection of 

therapies) 

. . . . 

22

Example: miRNA in USGENE 

L2 ANSWER 1 OF 2 USGENE COPYRIGHT 2012 SEQUENCEBASE CORP on STN 

AN 20100323357.173 USGENE 

TI MicroRNA Expression Profiling and Targeting in Peripheral Blood in 

Lung Cancer (PublishedApplication) 

DESC Artificial RNA; Synthetic oligonucleotide; sequence 173 of 206 

MTY RNA 

SQL 79 

Patent applicants often do not 

L2 ANSWER 2 OF 2 USGENE COPYRIGHT provide 2012 SEQUENCEBASE an informative CORP description. 

on STN 

AN 20100323357.172 USGENE 

TI MicroRNA Expression Profiling and Targeting in Peripheral Blood in 

Lung Cancer (PublishedApplication) 

DESC Artificial RNA; Synthetic oligonucleotide; sequence 172 of 206 

MTY RNA 

SQL 21 

Note: These sequences come from US20100323357, which 

is equivalent to WO2009070653 (previous slides). 

TRIAL format. 

23

Search example for CAplus and DWPI 

Search Question: 

Find recent patents that describe using siRNA 

therapeutically. 

24

Tips for searching in CAplus 

• Use both completely spelled out terms in 

addition to the acronym, e.g. for siRNA 

– Short interfering RNA, Small interfering RNA, 

Silencing RNA, siRNA, si RNA, siRNAi or siNA 

• Controlled terms (/CT) are available from 2007 

– siRNA, MicroRNA, RNA interference 

• Consider older related linked-terms to get 

enhanced retrieval prior to 2007 

– Double stranded RNA (L) small interfering/CT 

– RNA (L) microRNA/CT 

– Post-transcriptional processing (L) interference/CT 

25

=> FILE HCAPLUS 

Running the search in CAplus… 

=> S SHORT INTERFERING RNA OR SMALL INTERFERING RNA OR SIRNA OR 

SI RNA OR SINA OR SILENCING RNA OR (DOUBLE STRANDED RNA (L) 

SMALL INTERFERING) 

L1 51201 SHORT INTERFERING RNA OR SMALL INTERFERING RNA OR SIRNA OR 

SI RNA OR SINA OR SILENCING RNA OR (DOUBLE STRANDED RNA (L) 

SMALL INTERFERING) 

=> S L1 (L) (THU/RL OR ?THERAP?) 

L2 20385 L1 (L) (THU/RL OR ?THERAP?) 

=> S L2 AND PATENT/DT AND PY.B>2010 

L3 1517 L2 AND PATENT/DT AND PY.B>2010 

Use the (L) operator so that the 

search terms and therapeutic 

role are in the same /IT field. 

Use left and right truncation with the 

term Therap to pick up words, such as 

therapy, therapeutic, chemotherapy. 

Limit by patent document type 

(P/DT) and to recent basic 

patent publication years (PY.B). 

26

Example: CAplus record retrieved 

L3 ANSWER … OF 1517 HCAPLUS COPYRIGHT 2012 ACS on STN 

AN 2011:848465 HCAPLUS 

DN 155:144431 

TI Receptor tyrosine kinase-like orphan receptor 1 (ROR-1) inhibitors for 

treatment of cancer 

IN Mellstedt, Haakan; Rabbani, Hodjattallah; Teige, Ingrid 

PA Biolnvent International AB, Swed. 


CODEN: PIXXD2 

DT Patent 

LA English 

FAN.CNT 2 


--------------- ---- -------- -------------------- -------- 

PI WO 2011079902 A2 20110707 WO 2010-EP7524 20101210 

. . . . 

AB The invention relates to antibodies and siRNA mols. for inducing cell 

death by the specific binding of ROR1, domains thereof or nucleotide 

mols. encoding ROR1. The therapeutic inhibition of ROR-1 . . . . 

IT Antisense RNA 

Double stranded RNA 

siRNA 

BIB ABS HITIND display. 

The terms siRNA and therapeutic are in 

the abstract, and the Index Term fields. 

The terms siRNA and THU 

are linked in the IT field. 

RL: DMA (Drug mechanism of action); PAC (Pharmacological activity); 

PRP (Properties); THU (Therapeutic use); BIOL (Biological study); 

USES (Uses) 

(receptor tyrosine kinase-like orphan receptor 1 (ROR-1) inhibitors 

for treatment of cancer) 

27

Tips for searching in DWPI 

• As for CAplus, use both completely spelled out 

terms in addition to the acronym, e.g. for miRNA 

– MicroRNA, micro RNA, miRNA, mi RNA 

• Manual Codes (/MC) are available from 2005 

– siRNA: B04-E07C and D05-H12D8A 

– miRNA: B04-E07D and D05-H12D8B 

• Extend the search to find additional relevant results 

using the DWPI claims (/CLM) field, e.g. 

=> SET SFIELDS BI CLM (or: SET SFIELDS BI BIEX) 

• Option: focus a DWPI search using the mechanismof-action 

(/ACTN) abstract field, e.g. 

=> S ((RNA OR SIRNA OR MIRNA)(W)INTERFER? OR RNAI )/ACTN 

28

=> FILE WPIX 

Running the search in DWPI… 

=> SET SFIELDS BI CLM 

SET COMMAND COMPLETED 

=> S SHORT INTERFERING RNA OR SMALL INTERFERING RNA OR SIRNA OR 

SI RNA OR SINA OR SILENCING RNA OR B04-E07C/MC OR D05-H12D8A/MC 

B04-E07C SIRNA (SHORT INTERFERING RNA) 

D05-H12D8A SIRNA 

L4 8448 SHORT INTERFERING RNA/BI,CLM OR SMALL INTERFERING RNA/BI,CLM 

OR SIRNA/BI,CLM OR SI RNA/BI,CLM OR SINA/BI,CLM OR . . . . 

=> S L4 AND (?THERAP? OR ?TREAT? OR CURE? OR B14/MC) 

B14 PHARMACEUTICAL ACTIVITIES 

L5 7518 L4 AND (?THERAP?/BI,CLM OR ?TREAT?/BI,CLM OR CURE?/BI,CLM OR 

B14/MC) 

=> S L5 AND PY.B>2010 

L6 1437 L5 AND PY.B>2010 

Extend the search to find 

additional relevant results using 

the DWPI claims (/CLM) field. 

Limit to recent basic patent 

publication years (PY.B). 

29

Example: DWPI record retrieved 

L6 ANSWER … OF 1437 WPIX COPYRIGHT 2012 THOMSON REUTERS on STN 

AN 2011-F64480 [201135] WPIX 

CR 2006-252595 

BIB AB MC display. 

TI New purified small interfering RNA (siRNA) sequence, useful for 

modulating nuclear factor (NF)-kappa-B dependent gene transcription in 

a cell, and for treating inflammatory diseases and autoimmune 

diseases, e.g. osteoarthritis and asthma 

DC B04; D16 

IN CATRON K M; LI J; LI X 

PA (BOEH-C) BOEHRINGER INGELHEIM PHARM INC 

PIA US 20110124099 A1 20110526 (201135)* EN 27[10] 

siRNA and therapeutic are in the title, 

abstract, and Manual Code fields. 

. . . . 

AB US 20110124099 A1 UPAB: 20110605 

NOVELTY - A purified small interfering RNA (siRNA) sequence 

comprising fully defined 64 bp (SEQ ID NO. 1) given in the 

specification, is new. 

DETAILED DESCRIPTION - INDEPENDENT CLAIMS are: 

(1) an expression vector that expresses the siRNA; and . . . . 

ACTIVITY - Antiarthritic; Osteopathic; Vasotropic; . . . . 

MECHANISM OF ACTION - NF-Kappa-B-Modulator; Gene Therapy; 

RNA Interference; I-kappa-B-kinase-Alpha-Modulator; RNAi is indicated as a 

I-kappa-B-kinase-Beta-Modulator. 

therapeutic mechanism- 

USE - The siRNA is useful for modulating nuclear factor 

of-action (/ACTN). 

(NF)-kappa-B dependent gene transcription in a cell; and for treating 

inflammatory diseases and autoimmune diseases, . . . . . 

MC CPI: B04-E07C; B04-E08; B04-E99; B04-F11B1E; B14-C03; B14-C09; 

B14-C09A; B14-E08; B14-E10C1; B14-F05; B14-G02C; B14-G02D; 

B14-J01; B14-K01A; B14-N17C; B14-S01; B14-S03A; B14-S03C; 

D05-H12D8A; D05-H12E 

30

Agenda 








31

siRNA sequence search example 


Apart from WO2010083615, are there any other 

patent publications which have disclosed 

this siRNA, or other closely related sequences? 

5’-UGCUUAAAAGGGACAGUAUUC-3’ 

3’-CAACGAAUUUUCCCUGUCAUA-5’ 

32

Search Strategy for DGENE 

1) Run a GETSEQ sequence code match search 

for the siRNA sense and antisense strands 

2) Extend the search to the corresponding, closely 

related, DNA sequences (i.e. U -> T) 

3) Option: repeat the search in USGENE to find 

additional USPTO results 

4) Option: run a GETSIM similarity search to find 

other closely-related RNA or DNA sequences 

Note: in USGENE (and PCTGEN) it is also relatively common for RNA 

sequences to have Ts instead of Us (following the NCBI standard). 

33

Sequence code match search in DGENE 

=> FILE DGENE 

=> RUN GETSEQ AUACUGUCCCUUUUAAGCA|UGCUUAAAAGGGACAGUAU/SQSN 

. . . . 

Search simultaneously for the 

L1 RUN STATEMENT CREATED 

antisense and sense strands 

L1 5 AUACUGUCCCUUUUAAGCA|UGCUUAAAAGGGACAGUAU/SQSN 

using the pipe “|” symbol (L1). 

=> S L1 NOT WO2010083615/PN 

L2 0 L1 NOT WO2010083615/PN 

=> RUN GETSEQ ATACTGTCCCTTTTAAGCA|TGCTTAAAAGGGACAGTAT/SQSN 

. . . . 


L3 54 ATACTGTCCCTTTTAAGCA|TGCTTAAAAGGGACAGTAT/SQSN 

=> S L3 NOT WO2010083615/PN 

L4 52 L3 NOT WO2010083615/PN 

=> SOR L4 SQL A 

PROCESSING COMPLETED FOR L4 

L5 52 SOR L4 SQL A 

No additional answers are retrieved via 

the RNA search (L2), but some are 

retrieved via the DNA search, and sorted 

by sequence length (shortest first) (L5). 

34

=> D TRIAL ALIGN 1-2 


AN AUO55141 DNA DGENE 

TI New different expression construct library, useful for determining 

functional effect of DNA polymorphism or DNA mutation in posttranscriptional 

activity, and for determining impact of regulatory 

sequences in untranslated regions (UTRs). 

DESC Human UTR sequence, SEQ ID 2920. 

KW DNA library; untranslated region; UTR; translation; ds. 

SQL 187 

SEQ 

tgcttaaaag ggacagtat 

========== ========= 

HITS AT: 83-101 


AN AJT18724 cDNA DGENE 

TI New array comprising a transcriptome from a diseased tissue, useful 

for diagnosing a pathological condition or for determining 

responsiveness of a patient afflicted with a pathological condition 

to a therapeutic agent. 

DESC Human diseased liver tissue cDNA transcript SEQ ID NO:310368. 

KW Diagnosis; prognosis; screening; neoplasm; inflammation; . . . . 

SQL 451 

SEQ 

Review the additional records 

atactgtccc ttttaagca 

========== ========= 

HITS AT: 91-109 

Good DNA-based hits for the sense and 

antisense siRNA strands are retrieved. 

However, the additional hits are 

much longer than the query. 

35

Option: repeat the search in USGENE 

=> FILE USGENE 

=> RUN GETSEQ AUACUGUCCCUUUUAAGCA|UGCUUAAAAGGGACAGUAU|ATACTGTCCCT 

TTTAAGCA|TGCTTAAAAGGGACAGTAT/SQSN 

. . . . 


L6 76 AUACUGUCCCUUUUAAGCA|UGCUUAAAAGGGACAGUAU|ATACTGTCCC 

TTTTAAGCA|TGCTTAAAAGGGACAGTAT/SQSN 

=> SOR L6 SQL A 


L7 76 SOR L6 SQL A 

=> D TRI ALIGN 1-76 

L7 ANSWER … OF 76 USGENE COPYRIGHT 2012 SEQUENCEBASE CORP on STN 

TI Viral and viral associated MiRNAs and uses thereof 

(PublishedApplication) 

DESC Homo sapiens RNA; sequence 531403 

MTY RNA 

SQL 64 

SEQ 

ugcuuaaaag ggacaguau 

========== ========= 

HITS AT: 25-43 

=> D BRIEF 

Search simultaneously for the 

antisense strand, sense strand, and 

corresponding DNA sequences, 

using the pipe “|” symbol (L6). 

The results are sorted by 

sequence length (shortest 

first) before review (L7). 

36

Example: additional USGENE record 

L7 ANSWER … OF 76 USGENE COPYRIGHT 2012 SEQUENCEBASE CORP on STN 

AN 20070003575.531403 RNA USGENE 

TI Viral and viral associated MiRNAs and uses thereof . . . . 

IN Bentwich Itzhak (Rosh Haayin, IL); Avniel Amir . . . . 

PA NO ASSIGNEE AT PUBLICATION 

PI US 20070003575 A1 20070104 

AI US 2006-511035 20060828 

PRAI US 2006-511035 20060828 

WO 2005-IB2352 20050526 

US 2004-709739 20040526 

PSL SEQ ID NO 531403 

DESC Homo sapiens RNA; sequence 531403 

DT Patent 

AB Described herein are novel polynucleotides associated with viral 

infections. The polynucleotides are miRNAs . . . . 

ECLM US20070003575 A1: 1. An isolated nucleic acid comprising . . . . 

SSO NUCLEIC; PSIPS; APPLICATION 

ORGN Homo sapiens 

SQL 64 

SEQ 

1 aucuccaggg cugccccugu agguugcuua aaagggacag uauucucagu 

====== ========== === 

51 gcucuccuac ccca 

HITS AT: 25-43 

FEATURE TABLE: 

Key |Location| 

The sense strand of the siRNA 

query is a perfect match on this 

miRNA sequence in USGENE. 

Click this link to access the original sequence 

data as published via PSIPS (next slide). 

=======+========+========================================================== 

PSIPS | |http://www.sequencebase.com/psips.php?d=20070003575.531403 

37

Example: additional USGENE record (cont.) 

This is the source sequence data for the 

USGENE record on the previous slide. 

Note: “Human” is converted to “Homo 

sapiens” for USGENE records. 

38

=> FILE DGENE 

Option: run a similarity search 

=> RUN GETSIM AUACUGUCCCUUUUAAGCA/SQN BOTH BATCH 

PLEASE ENTER BATCH IDENTIFIER (MAX. 8 CHARS):SIRNA 

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 

RUN GETSIM AT 17:18:35 ON 09 AUG 2012 

COPYRIGHT (C) 2012 FIZ KARLSRUHE GMBH 

BATCH PROCESSING STARTED FOR SIRNA 

=> FIL STNG 

. . . . 

Run a FASTA-based similarity 

search with RUN GETSIM. 

Add BOTH to search the 

query and its complement 

simultaneously. 

Add BATCH to run the 

GETSIM search in offline 

BATCH mode. 

39

Example: BATCH notification email 

40

Retrieve the additional results 

=> FILE DGENE; RUN GETBATCH SIRNA 

. . . . 

8124 ANSWERS FOUND ABOVE A THRESHOLD OF 52 

QUERY SELF SCORE VALUE IS 95 

BEST ANSWER SCORE VALUE IS 95 

. . . . 

ENTER EITHER THE NUMBER OF ANSWERS YOU WISH TO KEEP 

OR ENTER MINIMUM PERCENT OF SELF SCORE FOLLOWED BY % 

(BEST ANSWER PERCENTAGE OF SELF SCORE IS 100%) 

ENTER (ALL) OR ? :80% 


L8 139 AUACUGUCCCUUUUAAGCA/SQN.BOTH 

Answer set arranged by accession number; to sort by descending 

similarity score, enter at an arrow prompt (=>) "sor score d". 

=> S L8 NOT WO2010083615/PN 

L9 121 L8 NOT WO2010083615/PN 

=> S L9 NOT (L1 OR L3) 

L10 70 L9 NOT (L1 OR L3) 

=> SOR SCORE D 


L11 70 SOR L10 SCORE D 

=> D TRIAL ALIGN 1-70 

Retrieve the results with 

RUN GETBATCH. 

Note: just the top 

scoring (≥ 80%) 

answers are chosen. 

The similarity search has retrieved 

additional results, which are sorted by 

sequence score (best first) (L11). 

41

Review the additional records 


AN AXC99315 cDNA DGENE 

TI New substantially purified nucleic acid molecule and its encoded 

polypeptides isolated from Sorghum, useful for producing a 

genetically transformed plant with improved properties, e.g. improved 

plant growth and development. 

DESC Sorghum bicolor cDNA sequence SEQ ID NO:23862. 

KW crop improvement; transgenic plant; plant growth regulant; . . . . 

SQL 604 

ALIGN Smith-Waterman score: 86 

19 na overlap starting at 97 (490 in complement) 

auacugucccuuuuaagca 

: ::.:.:::....::::: 

“In complement” indicates that 

aaactgtcccttttaagca 


AN AZF74667 DNA DGENE 

TI New compound targeted to a nucleic acid molecule encoding 

apolipoprotein C-III (Apo CIII), useful for treating a disease 

associated with Apo CIII, e.g. atherosclerosis, hyperlipidemia, 

diabetes, obesity and/or cardiovascular disease. 

DESC Human APOC3 mRNA inhibiting phosphorothioate oligonucleotide SEQID:78 

KW 2'-MOE wing; APOC3 gene; Apolipoprotein C3; anorectic; . . . . 

SQL 20 

ALIGN Smith-Waterman score: 85 

17 na overlap starting at 4 

auacugucccuuuuaag 

:.::.:.:::....::: 

atactgtcccttttaag 

this is a hit via the GETSIM 

complementary query. 

Note: unlike BLAST (later) 

GETSIM distinguishes 

between Ts and Us. 

42

miRNA sequence search example 


Are there any patent publications which disclose 

this miRNA, or similar RNA sequences (≥ 80%)? 

UACAGUACUGUGAUAACUGAA 

43

Search Strategy for DGENE, USGENE, 

PCTGEN and REGISTRY/CAplus 

1) RUN BLAST in DGENE, USGENE and PCTGEN 

using offline BATCH mode 

2) Repeat the search using CAS REGISTRY BLAST 

3) Retrieve, merge, organize by patent family, and 

display DGENE, USGENE and PCTGEN results 

4) Retrieve, identify and display unique CAplus 

references from the REGISTRY BLAST search 

5) Post-process DGENE, USGENE and PCTGEN 

results using the STN Express Table Tool 

6) Post-process unique REGISTRY BLAST results 

using the BLAST Report Tool 

44

NCBI recommended settings* for searching 

small sequence queries 

Peptide sequences 

• E-value: 20,000 • Matrix: PAM-30 

• Word size: 2 • Gap cost: 9 and 1 

Nucleotide sequences 

• E-value: 1,000 

• Word size: 7 

* http://www.ncbi.nlm.nih.gov/blast/Why.shtml 

• Matrix: Leave as is 

• Gap cost: n/a 

45

RUN BLAST searches in DGENE, USGENE and 

PCTGEN in offline BATCH mode 

=> FILE DGENE; RUN BLAST UACAGUACUGUGAUAACUGAA /SQN -F F -E 1000 

-W 7 BATCH 

Add BATCH to 

the end of the 

command. 

PLEASE ENTER BATCH IDENTIFIER (MAX. 8 CHARS):MIRNA 

. . . . 

BATCH PROCESSING STARTED FOR MIRNA 

=> FILE USGENE; RUN BLAST UACAGUACUGUGAUAACUGAA /SQN -F F -E 1000 

-W 7 BATCH 

Use the NCBI’s 

recommended 

BLAST settings. 


. . . . 

BATCH PROCESSING STARTED FOR MIRNA 

=> FILE PCTGEN; RUN BLAST UACAGUACUGUGAUAACUGAA /SQN -F F -E 1000 

-W 7 BATCH 


. . . . 

BATCH PROCESSING STARTED FOR MIRNA Tip: BATCH mode BLAST searches can 

be run concurrently in each database. 

46

Repeat using CAS REGISTRY BLAST 

a) Launch BLAST 

b) Search the sequence 

c) Examine and evaluate alignment/relevance of 

sequence answers 

d) Retrieve REGISTRY records on STN 

See also: Sequence Basics e-Seminar (May 2011): 

http://www.stn-international.com/Sequence_Basics_Seminar.html 

47

Adjust the REGISTRY BLAST settings for 

optimal search retrieval 

Increase the maximum 

number of answers to 1,000. 

Use the NCBI’s 

recommended 

BLAST settings. 

48

Retrieve references for sequences 

Note: in this 

example, BLAST 

sequences with 

scores of 34 or 

more (80% 

match or more) 

are selected. 

49

Retrieve REGISTRY results 

Get STN Data for records with BLAST scores of 34 or more (≥80%). 

=> FIL REGISTRY 

=> QUE (1319235-70-5 OR 1319788-38-9 OR 1322161-88-5 . . . . )/RN 

L1 QUE (1319235-70-5 OR 1319788-38-9 OR 1322161-88-5 . . . . )/RN 

=> QUE (1301790-19-1 OR 1309516-09-3 OR 1310781-96-4 . . . . )/RN 

L2 QUE (1301790-19-1 OR 1309516-09-3 OR 1310781-96-4 . . . . )/RN 

. . . . 

=> QUE (874419-11-1 OR 845594-31-2 OR 845700-64-3 . . . . )/RN 

L22 QUE (874419-11-1 OR 845594-31-2 OR 845700-64-3 . . . . )/RN 

=> S L1 OR L2 OR L3 OR L4 OR L5 OR L6 OR L7 OR L8 OR L9 OR L10 OR 

L11 OR L12 OR L13 OR L14 OR L15 OR L16 OR L17 OR L18 OR L19 

L23 250 L1 OR L2 OR L3 OR L4 OR L5 OR L6 OR L7 OR L8 OR L9 OR L10 OR 

L11 OR L12 OR L13 OR L14 OR L15 OR L16 OR L17 OR L18 OR L19 

=> S L20 OR L21 OR L22 

L24 35 L20 OR L21 OR L22 

=> S L23 OR L24 

L25 285 L23 OR L24 

285 similar sequences (L25) with 

BLAST scores of 34 or more. 

Commands within the dotted box 

are automatic commands. 

50

Retrieve REGISTRY results (cont.) 

=> S L25 AND SQL D SQIDE 



CN RNA, (U-A-C-A-G-U-A-C-U-G-U-G-A-U-A-A-C-U-G-A-A) (CA INDEX NAME) 


SQL 21 

NA 8 a 3 c 4 g 6 u 

SEQ 1 uacaguacug ugauaacuga a 

Here the search is 

refined further to 

short RNA (non-DNA) 

sequences (L27). 

An example of the 

type of a REGISTRY 

record retrieved. 

MF Unspecified 

CI MAN 

SR CA 

LC STN Files: CAPLUS 

DT.CA CAplus document type: Patent 

RL.P Roles from patents: ANST (Analytical study); BIOL (Biological 

study); PRP (Properties); USES (Uses) 

1 REFERENCES IN FILE CAPLUS (1907 TO DATE) 

51

Retrieve the DGENE results 

=> FILE DGENE; RUN GETBATCH MIRNA 

. . . . 



L28 424 UACAGUACUGUGAUAACUGAA/SQN.-F F -E 1000 -W 7 

=> S L28 AND SQL

Retrieve the USGENE and PCTGEN results 

=> FILE USGENE; RUN GETBATCH MIRNA 

. . . . 



L30 586 UACAGUACUGUGAUAACUGAA/SQN.-F F -E 1000 -W 7 

=> S L30 AND SQL S L32 AND SQL

Merge and review the DGENE, USGENE and 

PCTGEN BLAST search results 

=> SET DUPORDER FILE 

SET COMMAND COMPLETED 

=> DUP IDE L29 L31 L33 

. . . . 

FILE 'DGENE' ENTERED AT 22:24:23 ON 29 AUG 2011 

COPYRIGHT (C) 2011 THOMSON REUTERS 

FILE 'USGENE' ENTERED AT 22:24:23 ON 29 AUG 2011 

COPYRIGHT (C) 2011 SEQUENCEBASE CORP 

FILE 'PCTGEN' ENTERED AT 22:24:23 ON 29 AUG 2011 

COPYRIGHT (C) 2011 WIPO 

L34 435 DUP IDE L29 L31 L33 (INCLUDES 0 SETS OF DUPLICATES) 

ANSWERS '1-173' FROM FILE DGENE 

ANSWERS '174-372' FROM FILE USGENE 

ANSWERS '373-435' FROM FILE PCTGEN 

=> SOR SCORE D AN D 


L35 435 SOR L34 SCORE D AN D 

SET DUPORDER FILE ensures that 

multifile records merged using DUP 

IDE are organized by database (file). 

DUPLICATE IDENTIFY 

(DUP IDE) is used here 

to create a single 

multifile L-number (L34). 

The multifile L-number 

(L34) can be sorted by 

BLAST SCORE, or 

Percent Identity (IDENT). 

54

Use the STN Express 8.5 Patent Family 

Manager wizard to display the results 

Access the patent family 

manager wizard from the 

Discover! Menu. 

Choose a bibliographic display format with 

alignment for the first (best) hit. 

Option: choose a free-of-charge format with 

alignment for the rest of the family group. 

55

The patent family manager begins by organising 

the results using FSORT... 

=> FSORT L34 

. . . . 

L35 435 FSO L34 

Commands in RED are those 

issued automatically by the STN 

Express Patent Family Manager. 

62 Multi-record Families Answers 1-419 

Family 1 Answers 1-2 

FSORT organizes Family 2 Answers 3-4 

the patent 


sequence records Family 4 Answers 7-8 


by Publication, 

. . . . 

Application, 


Related, and Family 60 Answers 392-415 

Priority numbers. 



16 Individual Records Answers 420-435 

0 Non-patent Records In this example, 78 patent family 

. . . . 

groups (i.e. 62 + 16) are retrieved. 

56

...and then continues by displaying the family 

groups in the specified formats 

=> DIS L35 PFAM=1 1 BIB,SQL,SCORE,IDENT,ALIGN 

L35 ANSWER 1 OF 435 DGENE COPYRIGHT 2011 THOMSON REUTERS on STN FAMILY 1 

AN AZK14567 RNA DGENE 

TI Treating or preventing myocardial ischemia comprises modulating the 

expression or activity of microRNAs in the heart cells of the 

subject. 

IN Olson E N; Rooij E V; Quiat D 

PA (TEXA) UNIV TEXAS SYSTEM. 

PI WO 2011084460 A1 20110714 46 

AI WO 2010-US60460 20101215 

PRAI US 2009-286622P 20091215 

PSL Disclosure; SEQ ID NO 19 

DT Patent 

LA English 

OS 2011-J11773 [48] 

DESC Human ischemia regulated hsa-miR-101 miRNA, SEQ ID 19. 

SQL 21 

SCORE 42 100% of query self score 42 

IDENT 100% 

BLASTALIGN 

Query = 21 letters 

Length = 21 

Score = 42.1 bits (21), Expect = 6e-11 

Identities = 21/21 (100%) 

Strand = Plus / Plus 

Query: 1 tacagtactgtgataactgaa 21 

||||||||||||||||||||| 

Sbjct: 1 tacagtactgtgataactgaa 21 

Commands in RED are those 

issued automatically by the STN 

Express Patent Family Manager. 

Note: BLAST does not 

distinguish between Ts and 

Us. All Us in the query and 

answers are treated as Ts. 

57

...and then continues by displaying selected 

results in the specified formats (cont.) 


L35 ANSWER 392 OF 435 USGENE COPYRIGHT 2011 SEQUENCEBASE CORP on STN 

FAMILY60 

AN 20100047784.3920 RNA USGENE 

TI Method for detecting nucleic acids (PublishedApplication) 

IN Shlomit Gilad (Ganei Hadar, IL); Meiri Esther (Shoham, IL); 

Yerushalmi Noga (Nes Tziona, IL) 

PA ROSETTA GENOMICS LTD 

PI US 20100047784 A1 20100225 

AI US 2007-308954 20070629 

RLI WO 2007-IB3732 20070629 

PRAI US 2006-871095P 20061220 

. . . . 

PSL SEQ ID NO 3920 

DESC Xenopus tropicalis RNA; sequence 3920 of 21063 

DT Patent 

SQL 22 


IDENT 100% 

BLASTALIGN 


Length = 22 


Identities = 21/21 (100%) 



||||||||||||||||||||| 


This USGENE hit 

family was not found in 

the DGENE search. 

58

...and then continues by displaying selected 

results in the specified formats (cont.) 


L35 ANSWER 418 OF 435 PCTGEN COPYRIGHT 2011 WIPO on STN FAMILY 62 

AN 2011094335.649 RNA PCTGEN 

TI MicroRNA Signatures Predicting Responsiveness to Anti-HER2 Therapy 

PA Yale University 

Weidhaas, Joanne B. 

PI WO 2011094335 20110804 

RLI US 2010-298454P 20100126 

ED 20110804 

DT Patent 

SQL 21 


IDENT 100% 

BLASTALIGN 


Length = 21 


Identities = 21/21 (100%) 



||||||||||||||||||||| 


This PCTGEN hit 

family was not found in 

the DGENE search. 

59

Display unique CAplus answers including 

the HITRN for alignment post-processing 

=> FILE HCAPLUS 

Transfer Publication Numbers (PN) 

=> TRA L35 PN 

from DGENE, USGENE and PCTGEN 

L36 TRANSFER L35 1- PN : (L35) 143 to find TERMS corresponding HCAplus 

L37 92 L36 

records (L37). 

ALL TERMS IN L36 RETRIEVED. 

=> S L27 AND P/DT 

L38 79 L27 AND P/DT 

=> S L38 NOT L37 

L39 5 L38 NOT L37 

=> D BIB ABS HITRN 1-5 

The 285 REGISTRY records (L27) 

correspond to 79 HCAplus patent 

records (L38). 

In this example, five additional relevant 

references have been found by including 

a REGISTRY/CAplus search (L39). 

60

Example: CAplus record retrieved 

L39 ANSWER ... OF 5 HCAPLUS COPYRIGHT 2011 ACS on STN 

AN 2008:1508387 HCAPLUS 

DN 150:71776 

TI Reagents and methods for microRNA expression analysis and 

identification of cancer biomarkers 

IN Ahlquist, Paul Gerald; Sengupta, Srikumar; Den Boon, Johan Arie; 

Sugden, Bill; Newton, Michael Abbott 

PA Wisconsin Alumni Research Foundation, USA 


CODEN: PIXXD2 

DT Patent 

LA English 

FAN.CNT 1 

This unique HCAplus 

hit was not found in the 

DGENE,USGENE or 

PCTGEN searches. 


--------------- ---- -------- -------------------- -------- 

PI WO 2008154098 A2 20081218 WO 2008-US62938 20080507 

. . . . 

AB This invention provides methods for amplifying, Note: HITRN detecting, must be measuring, included, 

and identifying microRNAs from biol. samples, particularly . . . . 

so that the CAS REGISTRY 

IT 1093520-93-4 

RL: ADV (Adverse effect, including toxicity); BLAST ANT alignments (Analyte); can DGN be 

(Diagnostic use); PRP (Properties); ANST merged (Analytical into the study); BLAST BIOL Report. 

(Biological study); USES (Uses) 

(nucleotide sequence; reagents and methods for microRNA expression 

anal. and identification of cancer biomarkers) 

OSC.G 3 THERE ARE 3 CAPLUS RECORDS THAT CITE THIS RECORD (3 CITINGS) 

61

STN Express post-processing tools provide the 

finishing touches to the multi-file search 

2) 

1) DGENE, USGENE and PCTGEN results (L35) can be 

conveniently tabulated using the STN Express Table 

Tool and exported to a Microsoft Excel worksheet 

2) The REGISTRY “BLAST Report with Alignment data” 

tool merges BLAST alignments with corresponding 

unique CAplus records (L39) to form a single RTF file 

1) 

62

1) DGENE, USGENE and PCTGEN results 

can be tabulated and exported to Excel 

Preferred fields, fonts, 

labels, etc, can be 

saved as a Template 

for repeated re-use. 

63

Once in Excel there are various options to sort, 

filter and review the multi-file results 

Some tips for Microsoft Excel: 

• Resize columns and rows as desired – 

especially the BLAST alignment 

column width to approximately 77 

• View, Freeze panes – holds the top 

row fixed when scrolling down 

• Add Filters – provides a great way to 

navigate results – for example by 

BLAST percent identity (above) 

64

2) REGISTRY BLAST Alignments can be 

merged with corresponding CAplus records 

Preferred fields, fonts, 

labels, etc, can be 

saved as a Template 

for repeated re-use. 

REGISTRY BLAST alignments 

are merged with the CAplus 

records in the transcript. 

65

The REGISTRY “BLAST Report with Alignment 

data” tool provides an RTF file 

Download the post-processing template (.PRF) files used in this seminar: 

http://www.stn-international.com/stn_biosequence_searching_mfs.html 

66

Patent classifications for RNAi topics 

• IPC: C12N0015-113 /IPC 

– Non-coding nucleic acids modulating the expression of 

genes, e.g. antisense oligonucleotides 

• ECLA: C12N0015-113+NT /EPC 

– Non-coding nucleic acids modulating the expression of 

genes, e.g. antisense oligonucleotides; comment: 

Antisense DNA or RNA; Triplex- forming oligonucleotides; 

Catalytic nucleic acids, e.g. . . . 

• USPC: 536024500 /NCL 

– DNA/RNA fragments – nucleic acid expression inhibitors 

• USPC: 51404400A/NCL 

– Polynucleotides – antisense or RNA interference 

67

Summary 








68

Resources for sequence searching on STN 

• DGENE Workshop Manual 

http://www.stn-international.com/dgene_wm.html 

• USGENE Workshop Manual 

http://www.stn-international.com/usgene_wm.html 

• CAS REGISTRY sequence searching resources 

http://www.cas.org/support/stngen/stndoc/sequences.html 

• Multifile BLAST searching (step-by-step guide) 

http://www.stn-international.com/usgene_wm_mfs.html 

69

Recorded STN e-Seminars are available to 

watch at your own pace…. 

• FIZ Karlsruhe recorded e-Seminars: 

http://www.stn-international.com/recorded_events.html 

– Sequence Basics (all databases) 

– Multifile patent sequence searching (all databases) 

• CAS recorded e-Seminars: 

http://www.cas.org/support/stngen/stntraining/recorded.html 

– Sequence motif searching (all databases) 

– Processing sequence data (REGISTRY) 

– Unmasking the World of Antibodies (REGISTRY) 

70

CAS 

E-mail: help@cas.org 

Support and Training: 

www.cas.org 

For more information … 

FIZ Karlsruhe 

helpdesk@fiz-karlsruhe.de 

Support and Training: 

www.stn-international.de

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