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Sequence Code Match Searching Display the sequence details => D SQIDE L1 ANSWER 1 OF 1 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN AN AAW80589 peptide DGENE AA 2 A; 2 R; 0 N; 1 D; 0 B; 0 C; 1 Q; 1 E; 0 Z; 0 G; 0 H; 0 I; 2 L; 1 K; 0 M; 0 F; 1 P; 0 S; 0 T; 0 W; 0 Y; 0 V; 0 Others SQL 11 SEQ 1 rkdaerqlla p ========== = HITS AT: 1-11 FEATURE TABLE: Key |Location|Qualifier| ===============+========+=========+========================== Misc-difference|8 |note |"can be replaced with Ala" Misc-difference|9 |note |"can be replaced with Ala" Display the bibliographic details => D IBIB L1 ANSWER 1 OF 1 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN ACCESSION NUMBER: AAW80589 peptide DGENE Full-text TITLE: Detection of levels of T cell activation - by measuring increase in amount of serine phosphorylated Ick relative to total Ick as indicative of increased T cell activation INVENTOR: Madrenas J PATENT ASSIGNEE: (ROBA-N)ROBARTS RES INST JOHN P. PATENT INFO: WO 9846996 A2 19981022 48 APPLICATION INFO: WO 1998-IB801 19980410 PRIORITY INFO: US 1997-41878 19970411 PAT. SEQ. LOC: Claim 23; Page 27 DOCUMENT TYPE: Patent LANGUAGE: English OTHER SOURCE: 1998-583294 [49] DESCRIPTION: src-family tyrosine kinase peptide fragment. Page 106 | GENESEQ on STN (DGENE) Workshop Manual
Protein EXACT FAMILY Search Sequence Code Match Searching Search Question: Find out if the following 18 amino acid sequence has a patent reference: DVLFTTGLIRPVALVVDQ Search Strategy To find protein sequences in DGENE… Step 1 Try the sequence EXACT search Step 2 Run the sequence EXACT FAMILY search Step 3 Display the sequence and patent information Retrieve the sequence match => RUN GETSEQ DVLFTTGLIRPVALVVDQ/SQEP RUN GETSEQ AT 19:09:28 ON 30 DEC 2010 COPYRIGHT (C) 2010 FIZ KARLSRUHE GMBH L1 RUN STATEMENT CREATED L1 0 DVLFTTGLIRPVALVVDQ/SQEP => RUN GETSEQ DVLFTTGLIRPVALVVDQ/SQEFP RUN GETSEQ AT 19:11:02 ON 30 DEC 2010 COPYRIGHT (C) 2010 FIZ KARLSRUHE GMBH L2 RUN STATEMENT CREATED L2 1 DVLFTTGLIRPVALVVDQ/SQEFP Display the sequence and patent details => D IALL ALIGN GENESEQ on STN (DGENE) Workshop Manual | Page 107
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GENESEQ TM STN ® WORKSHOP MANUAL
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Contents DATABASE CONTENT .........
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DATABASE CONTENT In this section, y
Page 7 and 8:
How to read a DGENE record Database
Page 9 and 10:
Patent family and legal status info
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INTRODUCTION TO SIMILARITY SEARCHIN
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GETSIM Introduction to similarity s
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The uploaded sequence text file bec
Page 17 and 18:
Introduction to similarity searchin
Page 19 and 20:
Page 21 and 22:
Prepare the query offline Prepare y
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Sort the answers by descending simi
Page 25 and 26:
Display selected answers in a bibli
Page 27 and 28:
Prepare the query offline Prepare y
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Sort similarity score descending An
Page 31 and 32:
Page 33 and 34:
9590 ANSWERS FOUND ABOVE A THRESHOL
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Page 37 and 38:
RUN GETSIM for a SQN BOTH search In
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Upload the sequence and conduct a B
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Page 45 and 46:
ADVANCED SIMILARITY SEARCHING In th
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RUN BLAST Advanced similarity searc
Page 49 and 50:
BLAST advanced options Advanced sim
Page 51 and 52:
Altering BLAST parameters Advanced
Page 53 and 54:
Sort the answer set according to si
Page 55 and 56: 9913 ANSWERS FOUND BELOW EXPECTATIO
Page 57 and 58: Advanced similarity searching L4 AN
Page 59 and 60: Run a BLAST similarity search with
Page 61 and 62: Display some records with alignment
Page 63 and 64: Protein sequences: switching off th
Page 65 and 66: Sort similarity score descending An
Page 67 and 68: Display selected answers in a bibli
Page 69 and 70: Upload the sequence query text file
Page 71 and 72: Review the answers using IDENT and
Page 73 and 74: Display selected answers in a bibli
Page 75 and 76: RUN GETSIM using the translated (/T
Page 77 and 78: . . . . Advanced similarity searchi
Page 79 and 80: Batch Search Mode Advanced similari
Page 81 and 82: Collection of Batch Results Advance
Page 83 and 84: Current Awareness Alert Searching A
Page 85 and 86: CURRENT RESULTS AVAILABLE NAME RUN
Page 87 and 88: TEXT AND BIBLIOGRAPHIC In this sect
Page 89 and 90: Additional search indexes Text and
Page 91 and 92: Sorting answer sets Text and Biblio
Page 93 and 94: Prepare and save the query Prepare
Page 95 and 96: 341 ANSWERS FOUND BELOW EXPECTATION
Page 97 and 98: Text and Bibliographic searching Re
Page 99 and 100: Display selected answers in a prefe
Page 101 and 102: SEQUENCE CODE MATCH SEARCHING In th
Page 103 and 104: Sequence Code Match Searching Exact
Page 105: Protein EXACT Search GETSEQ search
Page 109 and 110: Protein SUBSEQUENCE Search Sequence
Page 111 and 112: Protein SUBSEQUENCE FAMILY Search S
Page 113 and 114: Nucleic acid EXACT Search Sequence
Page 115 and 116: Nucleic Acid SUBSEQUENCE Search Seq
Page 117 and 118: Using variability symbols Sequence
Page 119 and 120: Excluding residues Sequence Code Ma
Page 121 and 122: Repeat the search with the compleme
Page 123 and 124: APPENDICES This section includes ap
Page 125 and 126: Three letter codes 3-Letter Code 1-
Page 127 and 128: III: Universal Genetic Code Table A
Page 129 and 130: Nucleic acids Appendices Nucleotide
Page 131 and 132: Appendices Feature Definition termi
Page 133 and 134: Search fields VI: DGENE search and
Page 135 and 136: VII: Variability Symbols for GETSEQ
Page 137 and 138: VIII: BLAST advanced options Parame
Page 139 and 140: IX: Sequence Search Query Limits Ap
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