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ToStaden 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 Program Manual.
Any sequence file in GCG format can be converted with ToStaden into a format suitable for use in the Staden programs. GCG sequence symbols that aren't recognized by the Staden programs are converted to hyphens (-).
Here is a session using ToStaden to convert the sequence file test.seq into a Staden-format file:
% tostaden
TOSTADEN of what GCG sequence ? test.seq
Begin (* 1 *) ?
End (* 389 *) ?
What should I call the output file (* test.sdn *) ?
%
GCTGCCGCAGCGGCNGATGACAATAACRAYTGTTGCTGYGATGACGAYGA AGAGGARTTTTTCTTYGGTGGCGGAGGGGGNCATCACCAYATTATCATAA THAAAAAGAARTTGTTACTTCTCCTACTGTTRCTNYTAYTGYTRYTNATG AATAACAAYCCTCCCCCACCGCCNCAACAGCARCGTCGCCGACGGCGGAG AAGGCGNAGRMGAMGGMGRMGNTCTTCCTCATCGAGTAGCTCNAGYWSNA CTACCACAACGACNGTTGTCGTAGTGGTNTGGNNNTATTACTAYGAAGAG CAACAGSARTAATAGTGATARTRATRRABCD--GH--K-MN---RST-VW NY------abcd--gh--k-mn---rst-vwny------
ToStaden accepts a single nucleotide or protein sequence as input. Here is the input file for the example above:
!!NA_SEQUENCE 1.0
This sequence contains every symbol in the alphabet of
legitimate GCG sequence characters (Appendix III).
Test.Seq Length: 389 January 7, 1996 21:57 Type: N Check: 3365 ..
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*@&~.
<ends with
all lowercase sequence characters<
The function of ToStaden 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.
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. GCGToBLAST creates a database that can be searched by the BLAST program from any set of sequences in GCG 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.
All parameters for this program may be put on the command line. Use the parameter -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 parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
Minimal Syntax: % tostaden [-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
None.
None.
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