note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
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Contents<br />
DATABASE CONTENT ............................................................................................................................................. 5<br />
DATABASE CONTENT ........................................................................................................................................................... 6<br />
INTRODUCTION TO SIMILARITY SEARCHING ........................................................................................................ 11<br />
SIMILARITY SEARCHING ..................................................................................................................................................... 12<br />
HOW TO USE GETSIM AND BLAST .................................................................................................................................... 14<br />
SIMILARITY SEARCHING WITH BLAST ................................................................................................................................... 20<br />
SIMILARITY SEARCHING WITH GETSIM ................................................................................................................................ 32<br />
SIMILARITY SEARCHING AND FSORT .................................................................................................................................... 40<br />
ADVANCED SIMILARITY SEARCHING .................................................................................................................... 45<br />
SIMILARITY SEARCHING IN DGENE ...................................................................................................................................... 46<br />
BLAST ADVANCED OPTIONS ............................................................................................................................................... 49<br />
ALTERING BLAST PARAMETERS .......................................................................................................................................... 51<br />
SORTING BY BLAST PERCENT IDENTITY (IDENT) .................................................................................................................... 68<br />
TRANSLATED PROTEIN SIMILARITY SEARCH ............................................................................................................................. 74<br />
BATCH SEARCH MODE ...................................................................................................................................................... 79<br />
CURRENT AWARENESS ALERT SEARCHING ............................................................................................................................. 83<br />
TEXT AND BIBLIOGRAPHIC SEARCHING ................................................................................................................ 87<br />
INTRODUCTION ................................................................................................................................................................ 88<br />
REFINING A BLAST SEARCH WITH TEXT OR DATE TERMS ........................................................................................................... 92<br />
SEQUENCE CODE MATCH SEARCHING ................................................................................................................ 101<br />
SEQUENCE CODE MATCH SEARCHING ................................................................................................................................ 102<br />
GETSEQ SEARCH OPTIONS .............................................................................................................................................. 105<br />
USING VARIABILITY SYMBOLS ............................................................................................................................................ 117<br />
COMPLEMENTARY NUCLEIC ACID SEARCHING ...................................................................................................................... 120<br />
APPENDICES ...................................................................................................................................................... 123<br />
I: AMINO ACID CODES .................................................................................................................................................... 124<br />
II: NUCLEOTIDE CODES .................................................................................................................................................... 126<br />
III: UNIVERSAL GENETIC CODE TABLE ................................................................................................................................. 127<br />
IV: FEATURE KEYS IN DGENE FEATURE TABLES .................................................................................................................... 128<br />
V: MOLECULE TYPE CODES .............................................................................................................................................. 132<br />
VI: DGENE SEARCH AND DISPLAY FIELDS ............................................................................................................................ 133<br />
VII: VARIABILITY SYMBOLS FOR GETSEQ ........................................................................................................................... 135<br />
VIII: BLAST ADVANCED OPTIONS ...................................................................................................................................... 137<br />
IX: SEQUENCE SEARCH QUERY LIMITS ................................................................................................................................ 139<br />
GENESEQ on STN (DGENE) Workshop Manual | Page 3
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