readme.dna

unix或linux下的DNA分析软件源码 其功能如下 1. Edit up to 256 peptide or DNA sequences simultaneously. 2. Transla

   DNA 
   Latest Version: 1.1.0 (May 6, 2000)
   
   Thomas Nelson ([e-mail], [e-mail])
   
   DNA is a miscellaneous collection of utilities for handling sequence data
   in Linux. The programs should compile without difficulty in any Unix
   system (type 'make'). If desired, they can be manually copied to some
   suitable location, e.g., /usr/local/bin.
   
   These programs were written to remedy deficiencies in other, more complete
   packages. No attempt was made to replicate the complete functionality of 
   programs like SeqLab. However, if you find a bug, please notify me and I
   will post an updated version. If you would like to contribute a useful
   utility of your own, let me know and I will include it in the package. 
   These programs can be freely distributed and altered provided that any 
   altered version is clearly indicated as such. 
   
   So far the package consists of the following:
   
   dna - Motif-based sequence editor. Has the following features:
      1. Edit up to 256 peptide or DNA sequences simultaneously.
      2. Translates DNA->protein; click 'next' to display next frame.
      3. Dot matrix plot of any 2 sequences.
      4. Rudimentary amino acid statistics (MW and amino acid percentage)
      5. Saves matrix plot as PBM image format.
      6. Sequence reversal.
      7. Creates alignment file for 'highlight' (below).
      8. Tab key toggles editing of next sequence.
      Various display parameters can be changed by editing the configuration 
      file ~/.dna/dna.ini. Motif and X parameters can be set in ~/.Xdefaults.
      See X documentation for details on .Xdefaults.

      Printing requires pnmtops (which is part of the netpbm package) to 
      be on your system. This can be downloaded from 
                http://download.sourceforge.net/netpbm
      (this package in turn also requires libpng).

   dnatrans - Converts DNA or RNA to protein. All 6 strands are translated,
      written to separate files, and given suffixes of '.1' to '.6'. They
      are also printed to the screen.
   
   seqrev - converts sense<->antisense. The output strand is written from
      5'->3'.
      
   highlight - displays multiple sequences and creates a PostScript file
      showing identical bases or related bases/amino acids highlighted.
      Highlight does not create an alignment, it merely creates an output
      file suitable for inclusion in a LaTeX document or for printing.
      The file can be viewed with 'gv' or 'gs' or printed on a PostScript
      printer.
      
      The questions asked by 'highlight' are:
      
      Controlling sequence - The sequence to which similarities are
         to be compared. Can be:
         1. 1st - only matches to the top sequence are highlighted.
         2. 1st+2nd - matches to the first or 2nd sequence are highlighted.
         3. Any - All identities in each position are highlighted.
            For example, if two sequences contain a 'D', and two others
            contain a 'R' at that position, both D and R are highlighted. 
         4. Highest - Only the matches that are present in the greatest
            number of sequences (i.e., the consensus) are highlighted. 
            If two of these exist, only the first one is highlighted.
            For example, if the first 3 sequences contain 'M' and the 
            next 3 contain 'A', only the 'M's will be highlighted. Feel
            free to change this if you don't like it.
         5. Next - Each sequence is compared with the one that comes
            after it.

       Enter 1=identity 2=homology - If 'identity' is selected, the positions
            must be identical. If 'homology' is selected, the following 
            homologies are assumed:
                    D is homologous to E 
                    Q is homologous to N
                    F is homologous to W or Y
                    I is homologous to L
                    K is homologous to R
                    S is homologous to T
            Note that the homologies are all symmetric. The homologies are
            conservative. For example, aspartate and asparagine are considered 
            non-homologous, as are glutamate and glutamine. This is obviously
            not desirable if the results are from an Edman, and is easy to 
            change if you don't like it. Well maybe not easy but possible.
                                        

       Font - Can be any valid PostScript font name, for example:
            Helvetica
            Helvetica-Oblique
            Helvetica-Bold
            Times-Roman
            Courier
       Do a 'strings /usr/bin/gs' for a complete list. Any font, including
          proportional fonts, will work, but Courier and Helvetica are the
          traditional choices for sequences.
            
       BW/Color  - selects whether color or grayscale should be used.
       
       Normal character RGBcolor, etc. - If 'color' is selected, change these
          values to define the color to use. There must be 3 numbers between
          0 and 1 where 0 is no color and 1 is the maximal color. For example,
                         0.000 0.500 1.000
          will create a color with no red, 50% of green, and 100% of the
          maximum possible blue.

       Normal character gray value, etc. - If 'B/W' is selected, change these
          values to define the grayscale value to use. This must be one number
          between 0 and 1. For example,  
                           0.500
          will create a medium gray.
          
       Hitting <Enter> will accept the default value. If you change the color,
          be sure to enter the parameter in the correct format, otherwise
          the Postscript file will be invalid and you will not get any printout. 
          Needless to say, care should be taken to make sure the character color
          and the background colors are different.
   
       Spacing between chunks - The sequences are wrapped if they are wider
          than a page width. This parameter sets the spacing between wrapped
          groups of sequences.
          
       Chunks per page - Number of wrapped groups of sequences per page. 



        
    All the programs except 'highlight' take raw sequences as input. Lines
    containing documentation or comments must start with a hash mark '#'.
    Thus, if your data are in EMBL format, the sequences must be stripped
    out or prefaced with a '#'. Spaces, punctuation marks, and digits are ignored.
    
    Highlight requires data in the following format:
      o 1 sequence per line
      o Sequence name is at the beginning of each line
      o A vertical bar separates the name from the sequence data
      o Maximum of 1000 sequences total, of 10000 characters each. (This
        can be easily changed).
      o Everything between the lines "SEQUENCES" and "END" is considered to
        be a sequence. Everything outside this is a label.
      o Labels can be BOX, TITLE, COMMENT, LABEL, or TEXT. There can be a total
        of 1000 labels of any type.
          TITLE - is followed by the title
          BOX - followed by starting x position, ending x position, starting
                sequence no., and ending sequence no. The box is drawn to 
                include all the indicated characters.
          COMMENT - is ignored
          LABEL - followed by starting x position and starting sequence 
                position. These do not have to be valid numbers; for example
                LABEL 2 0 will draw a label above the sequences starting at
                the 2nd character in the sequence. Label is drawn in the same 
                font as sequence names.
          TEXT - followed by a starting y position in sequence units. Similar 
                to LABEL, except that the x label positions are obtained
                from its position in the text string. This makes it easier to 
                align a label with a specific sequence element, since the 
                label can be placed directly above the position being labeled.
                Label is drawn in the same font as sequence names and is
                printed left-justified starting at the position at which it
                appears in the text string. Successive labels must be separated
                by two or more spaces. Labels are not truncated at the end of
                a line, so they can extend past the end of the sequence.

    For example: 
    
    
        TITLE Alignment of calcium-binding proteins
        BOX 100 120 1 4
        BOX 21 31 1 16
        COMMENT The above will draw a box around DFQ..RV- down to -YRG..IV-
        BOX 204 215 1 16
        BOX 322 324 1 1
        COMMENT This is a comment
        LABEL 10 0 This is a label above the M in the first sequence
        # The next line will put labels above the first sequence (1=cp20b)
        TEXT 0                       The LS motif     The FNTFY motif
        # The next line will numbers below the last (16th) sequence
        # Note, each number must be separated by 2 spaces otherwise they
        # will be spaced incorrectly.
        TEXT 17               10        20        30        40   

        SEQUENCES
        calexcitin  |         MA-AHQ LS- DFQRNKILRV-  FNTFY DC ...
        scp2.pep    |      KKKTNTIMS IS- DFRKKKLLFL-  FNVFF DV
        f56d1.6     |    MVVAKPTAAVS IE- DLIKKHSDVDP  FLVKK --
        kchip1      |       ..YAQFFP HG- DASTYAH-YL-  FNAF- DT
        kchip2      |       ..YSQFFP QG- DSSTYAT-FL-  FNAF- DT
        kchip3      |       ..YAQFFP QG- DATTYAH-FL-  FNAF- DA
        kip2        |      MGNKQTIFT EE  QLDNYQ DCTF  FN KK DI
        frequenin   |      MG KK SSK LKQ-DTIDRLTTDTY  F-TEK EI
        neurocalcin |      MG K QNSK LAP EVMEDLVKSTE  FN-EH EL
        c18b11.04-  |      MG KSQ SK LSQ DQLQDLVRSTR  FD-KK EL
        redb        |        KRET WQ TS- EHAGRD-----  TSRHS MA
        caltractin  |   MARRGQQPPPQQAPPAQKNQTGK ---   FNPA- EF
        calcyphosine|MDAVDATVEKLRAQC LSR GALGIQGLAR-  FFRRL D-
        calretinin  |        ..KYDK  NS  DGKIEMAELAQI LPTEENFL
        oncomodulin |        -MSITDI LS  AEDIAAA L QE CQ      
        gpxa_neime  |GNAVD---------- LSG -YRGKVLLIV-  -NTAT --

        END


    Any other characters such as '.', '-' are printed as they appear but
    do not influence whether a position is highlighted.