1Index a GCG formatted database using b+tree indices 2Version: EMBOSS:6.6.0.0 3 4 Standard (Mandatory) qualifiers: 5 [-dbname] string Basename for index files (Any string from 2 6 to 19 characters, matching regular 7 expression /[A-z][A-z0-9_]+/) 8 [-dbresource] string Resource name (Any string from 2 to 19 9 characters, matching regular expression 10 /[A-z][A-z0-9_]+/) 11 -idformat menu [SWISS] Entry format (Values: EMBL (EMBL); 12 SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew); 13 GENBANK (Genbank, DDBJ); PIR (NBRF)) 14 -directory directory [.] Database directory 15 -filenames string [*.seq] Wildcard database filename (Any 16 string) 17 -fields menu [id,acc] Index fields (Values: id (ID); acc 18 (Accession number); sv (Sequence Version and 19 GI); des (Description); key (Keywords); org 20 (Taxonomy)) 21 -[no]compressed boolean [Y] Compressed index files 22 -outfile outfile [*.dbxgcg] General log output file 23 24 Additional (Optional) qualifiers: (none) 25 Advanced (Unprompted) qualifiers: 26 -release string [0.0] Release number (Any string up to 9 27 characters) 28 -date string [00/00/00] Index date (Date string dd/mm/yy) 29 -exclude string Wildcard filename(s) to exclude (Any string) 30 -statistics boolean [N] Report I/O statistics for each input 31 file 32 -indexoutdir outdir [.] Index file output directory 33 34 Associated qualifiers: 35 36 "-directory" associated qualifiers 37 -extension string Default file extension 38 39 "-indexoutdir" associated qualifiers 40 -extension string Default file extension 41 42 "-outfile" associated qualifiers 43 -odirectory string Output directory 44 45 General qualifiers: 46 -auto boolean Turn off prompts 47 -stdout boolean Write first file to standard output 48 -filter boolean Read first file from standard input, write 49 first file to standard output 50 -options boolean Prompt for standard and additional values 51 -debug boolean Write debug output to program.dbg 52 -verbose boolean Report some/full command line options 53 -help boolean Report command line options and exit. More 54 information on associated and general 55 qualifiers can be found with -help -verbose 56 -warning boolean Report warnings 57 -error boolean Report errors 58 -fatal boolean Report fatal errors 59 -die boolean Report dying program messages 60 -version boolean Report version number and exit 61 62