EToStaden writes a GCG sequence into a file in Staden format. If the file contains a nucleotide sequence, the ambiguity codes are converted as shown in Appendix III of the GCG Program Manual. EToStaden is a version of GCG's ToStaden with command line control.
Any sequence file in GCG format can be converted with EToStaden into a format suitable for use in the Staden programs. If the sequence is a nucleic acid sequence, the compatible ambiguity codes are converted from the IUB-IUPAC versions to Staden's versions. You can see how they are converted in Appendix III or in the example below.
This GCG program was modified by Jaakko Hattula (Tampere University of Technology, Finland) and Peter Rice (E-mail: firstname.lastname@example.org Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).
All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (email@example.com).
Here is a session using EToStaden to convert the sequence file test2.seq (which you can fetch as EGenDocData:test2.seq) into a Staden-format file:
% etostaden ETOSTADEN uses any sequence data ETOSTADEN of what sequence ? test2.seq Start (* 1 *) ? End (* 389 *) ? What should I call the output file (* test2.sdn *) ? %
Here is the output file test.sdn:
GCTGCCGCAGCGGC-GATGACAATAACRAYTGTTGCTGYGATGACGAYGA AGAGGARTTTTTCTTYGGTGGCGGAGGGGG-CATCACCAYATTATCATAA T-AAAAAGAARTTGTTACTTCTCCTACTGTTRCT-YTAYTGYTRYT-ATG AATAACAAYCCTCCCCCACCGCC-CAACAGCARCGTCGCCGACGGCGGAG AAGGCG-AGR5GA5GG5GR5G-TCTTCCTCATCGAGTAGCTC-AGY78-A CTACCACAACGAC-GTTGTCGTAGTGGT-TGG---TATTACTAYGAAGAG CAACAG8ARTAATAGTGATARTRATRRA-C---G--6-5---R8TT-7-Y ---A-C---G--6-5---R8TT-7-Y---
The following programs convert sequences between other formats and GCG format: FromEMBL, FromGenBank, FromIG, FromPIR, FromStaden, FromFastA, ToIG, ToPIR, ToStaden and ToFastA.
DataSet creates a GCG data library from any set of sequences in GCG format. ToBLAST creates a database that can be searched by the BLAST program from any set of sequences in GCG format.
The ambiguity codes are not all strictly comparable in converting from GCG to Staden format. All documentation and numbering is lost in the Staden-format output file. You should be sure that the Staden program you intend to use is compatible with any ambiguity codes used in your sequence.
Here is the input file for the example above:
This sequence contains every symbol in the alphabet of legitimate GCG sequence characters (Appendix III). Test.Seq Length: 389 July 19, 1994 15:05 Type: N Check: 8468 .. 1 >starts with the codons from appendix iii> GCTGCCGCAG CGGCXGATGA CAATAACRAY TGTTGCTGYG ATGACGAYGA 51 AGAGGARTTT TTCTTYGGTG GCGGAGGGGG XCATCACCAY ATTATCATAA 101 THAAAAAGAA RTTGTTACTT CTCCTACTGT TRCTXYTAYT GYTRYTXATG 151 AATAACAAYC CTCCCCCACC GCCXCAACAG CARCGTCGCC GACGGCGGAG 201 AAGGCGXAGR MGAMGGMGRM GXTCTTCCTC ATCGAGTAGC TCXAGYWSXA 251 CTACCACAAC GACXGTTGTC GTAGTGGTXT GGXXXTATTA CTAYGAAGAG 301 CAACAGSART AATAGTGATA RTRATRR >continues with all uppercase sequence characters> ABC DEFGHIJKLM NOPQRSTUVW 351 XYZ.+@&*ab cdefghijkl mnopqrstuv wxyz*@&+.
The function of EToStaden depends on whether your input sequence(s) are protein or nucleotide. Programs determine the type of a sequence by the presence of either Type: N or Type: P on the last line of the text heading just above the sequence. If your sequence(s) are not the correct type, turn to Appendix VI for information on how to change or set the type of a sequence.
All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.
Minimal Syntax: % etostaden [-INfile1=]test.seq -Default Prompted Parameters: -BEGin=1 -END=389 range of interest [-OUTfile1=]test.sdn output file name Local Data Files: None Optional Parameters: None
LOCAL DATA FILES
Printed: April 22, 1996 15:53 (1162)