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Advanced similarity searching Run a BLAST search with altered settings => RUN BLAST GSSFLSPEHQR/SQP -W 2 -F F -E 20000 -M PAM30 BLAST Version 2.2 The BLAST search is adjusted with the NCBI recommended settings for short amino acid The BLAST software is used herein with permission sequence of queries theNational (see Helpful Center HINT above). for Biotechnology Information (NCBI) of the National Library of Medicine (NLM). . . . . 7053 ANSWERS FOUND BELOW EXPECTATION VALUE OF 20000.0 QUERY SELF SCORE VALUE IS 38 BEST ANSWER SCORE VALUE IS 38 Similarity Score 38 ||||| ||||| ||||||| ||||||| ||||||||| ||||||||| ||||||||||| ||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||| 19 |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| Answer Count 1420 2840 4260 5680 7100 ENTER EITHER THE NUMBER OF ANSWERS YOU WISH TO KEEP OR ENTER MINIMUM PERCENT OF SELF SCORE FOLLOWED BY % The BLAST settings can be (BEST ANSWER PERCENTAGE OF SELF SCORE IS 100%) seen associated with the RUN ENTER (ALL) OR ? :ALL command L-number (L1). L1 RUN STATEMENT CREATED L1 7053 GSSFLSPEHQR/SQP.-W 2 -F F -E 20000 -M PAM30 Answer set arranged by accession number; to sort by descending similarity score, enter at an arrow prompt (=>) "sor score d". => Sort the answer set according to similarity score => SOR SCORE D PROCESSING COMPLETED FOR L1 L2 7053 SOR L1 SCORE D Page 60 | GENESEQ on STN (DGENE) Workshop Manual Using the appropriate BLAST settings, 7053 answers are retrieved.
Display some records with alignment => D TRIAL SCORE ALIGN 1 100 200 Advanced similarity searching L3 ANSWER 1 OF 7053 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN AN AYG94438 protein DGENE TI New isolated extended recombinant polypeptide e.g. having non-repetitive amino acid sequence, useful for treating a disease (e.g. obesity and multiple sclerosis) and improving property (e.g. terminal half-life) of a protein e.g. exendin-4. DESC BPXTEN polypeptide sequence SEQ ID 1285. KW Fusion protein; XTEN protein; acquired immune deficiency syndrome; anorectic; antianginal; antiarthritic; antiinflammatory; . . . . SQL 893 SCORE 38 100% of query self score 38 BLASTALIGN Query = 11 letters Length = 893 Score = 37.5 bits (81), Expect = 3e-08 Identities = 11/11 (100%), Positives = 11/11 (100%) Query: 1 GSSFLSPEHQR 11 GSSFLSPEHQR Sbjct: 866 GSSFLSPEHQR 876 L3 ANSWER 100 OF 7053 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN AN AQD01839 protein DGENE TI New collection of matched biological reagents comprises at least 100 sets of matched biological reagents, where each set is associated with a different target biomolecule, useful for identifying matched reagents. DESC Ghrelin precursor protein. KW bioinformatics; protein targeting; BOND_PC; ghrelin/obestatin . . . . SQL 117 SCORE 38 100% of query self score 38 BLASTALIGN Query = 11 letters Length = 117 Score = 37.5 bits (81), Expect = 4e-09 Identities = 11/11 (100%), Positives = 11/11 (100%) Query: 1 GSSFLSPEHQR 11 GSSFLSPEHQR Sbjct: 24 GSSFLSPEHQR 34 L3 ANSWER 200 OF 7053 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN AN AEE25309 peptide DGENE TI Novel monoclonal antibody to endocannabinoid molecule or specific peptide, useful for preparing medicament for treating obesity, anorexia or loss of appetite and for disrupting and modulating cell signaling events to therapeutic effect. DESC Ghrelin hormone peptide #2 useful for generating a monoclonal antibody. KW monoclonal antibody; screening; pharmaceutical; obesity; . . . . SQL 28 SCORE 38 100% of query self score 38 BLASTALIGN Query = 11 letters Length = 28 Score = 37.5 bits (81), Expect = 2e-09 Identities = 11/11 (100%), Positives = 11/11 (100%) Query: 1 GSSFLSPEHQR 11 GSSFLSPEHQR Sbjct: 1 GSSFLSPEHQR 11 GENESEQ on STN (DGENE) Workshop Manual | Page 61
Page 1 and 2:
GENESEQ TM STN ® WORKSHOP MANUAL
Page 3 and 4:
Contents DATABASE CONTENT .........
Page 5 and 6:
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
Page 11 and 12: INTRODUCTION TO SIMILARITY SEARCHIN
Page 13 and 14: GETSIM Introduction to similarity s
Page 15 and 16: The uploaded sequence text file bec
Page 17 and 18: Introduction to similarity searchin
Page 21 and 22: Prepare the query offline Prepare y
Page 23 and 24: 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
Page 29 and 30: Sort similarity score descending An
Page 33 and 34: 9590 ANSWERS FOUND ABOVE A THRESHOL
Page 37 and 38: RUN GETSIM for a SQN BOTH search In
Page 41 and 42: Upload the sequence and conduct a B
Page 45 and 46: ADVANCED SIMILARITY SEARCHING In th
Page 47 and 48: 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: Run a BLAST similarity search with
Page 63 and 64: Protein sequences: switching off th
Page 65 and 66: Sort similarity score descending An
Page 69 and 70: Upload the sequence query text file
Page 71 and 72: Review the answers using IDENT and
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 and 106: Protein EXACT Search GETSEQ search
Page 107 and 108: Protein EXACT FAMILY Search Sequenc
Page 109 and 110: Protein SUBSEQUENCE Search Sequence
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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
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Excluding residues Sequence Code Ma
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Repeat the search with the compleme
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APPENDICES This section includes ap
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Three letter codes 3-Letter Code 1-
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III: Universal Genetic Code Table A
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Nucleic acids Appendices Nucleotide
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Appendices Feature Definition termi
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Search fields VI: DGENE search and
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VII: Variability Symbols for GETSEQ
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VIII: BLAST advanced options Parame
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IX: Sequence Search Query Limits Ap
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