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Appendices I: Amino Acid Codes The following table lists the 1- and 3-letter codes 1 that may be used for the common amino acids DGENE in sequence searches using RUN GETSEQ (page 102). Uncommon amino acids are represented in the sequence either by a related parent amino acid, if available, or by an 'X'. Details about uncommon amino acids in a sequence will typically be found in the feature table (FEAT). DGENE uses standard abbreviations for most non-standard amino acids as proposed by the US Patent and Trade Mark Office (US Official Gazette May 16 th , 1989) 2 . One letter codes 1-Letter Code 3-Letter Code Name ------------- ------------- ---- A Ala Alanine B Asx Aspartic acid or Asparagine C Cys Cysteine D Asp Aspartic acid E Glu Glutamic acid F Phe Phenylalanine G Gly Glycine H His Histidine I Ile Isoleucine K Lys Lysine L Leu Leucine M Met Methionine N Asn Asparagine P Pro Proline Q Gln Glutamine R Arg Arginine S Ser Serine T Thr Threonine V Val Valine W Trp Tryptophan X Xxx Uncommon, unknown or other (Xaa) Y Tyr Tyrosine Z Glx Glutamic acid or Glutamine <strong>note</strong> The codes B and Z may be used only in subsequence family searches /SQSFP). B and Z match both the specific amino acids and the generic B and Z in the database. 1 The assignment of the symbols follows the IUPAC/IUB rules. Joint Commission on Biochemical Nomenclature (JCBN) Nomenclature and Symbolism for Amino Acids and Peptides. Recommendations 1983. Eur.J.Biochem.138:9- 37(1984) 2 See: http://www.uspto.gov/web/offices/pac/mpep/documents/appxr_1_821.htm. Page 124 | GENESEQ on STN (DGENE) Workshop Manual
Three letter codes 3-Letter Code 1-Letter Code Name ------------- ------------- ---- Ala A Alanine Arg R Arginine Asn N Asparagine Asp D Aspartic acid Asx B Aspartic acid or Asparagine Cys C Cysteine Gln Q Glutamine Glu E Glutamic acid Glx Z Glutamic acid or Glutamine Gly G Glycine His H Histidine Ile I Isoleucine Leu L Leucine Lys K Lysine Met M Methionine Phe F Phenylalanine Pro P Proline Ser S Serine Thr T Threonine Trp W Tryptophan Tyr Y Tyrosine Val V Valine Xxx X Uncommon <strong>note</strong> The codes Asx and Glx may be used only in subsequence family searches (/SQSFP). Asx and Glx match both the specific amino acids and the generic Asx and Glx in the database. Appendices GENESEQ on STN (DGENE) Workshop Manual | Page 125
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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
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How to read a DGENE record Database
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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
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Introduction to similarity searchin
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Prepare the query offline Prepare y
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Sort the answers by descending simi
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Display selected answers in a bibli
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Prepare the query offline Prepare y
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Sort similarity score descending An
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9590 ANSWERS FOUND ABOVE A THRESHOL
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RUN GETSIM for a SQN BOTH search In
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Upload the sequence and conduct a B
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ADVANCED SIMILARITY SEARCHING In th
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RUN BLAST Advanced similarity searc
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BLAST advanced options Advanced sim
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Altering BLAST parameters Advanced
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Sort the answer set according to si
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9913 ANSWERS FOUND BELOW EXPECTATIO
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Advanced similarity searching L4 AN
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Run a BLAST similarity search with
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Display some records with alignment
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Protein sequences: switching off th
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Sort similarity score descending An
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Upload the sequence query text file
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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 and 106: Protein EXACT Search GETSEQ search
Page 107 and 108: Protein EXACT FAMILY Search Sequenc
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: APPENDICES This section includes ap
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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note - FIZ Karlsruhe

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