Otherware/Otherware_1_SB_Development.iso/mac/misc/medical/dna_stac.cpt/dnastack.readme

Text File | 1992-07-30 | 11.6 KB | 198 lines

Features of DNA Translator and Aligner HyperCard 2.0 stacks
Version 1.0k 6/14/92 Copyright 1990,1991,1992 D. J. Eernisse
Email: [e-mail] (internet) or usergdef@umichum (bitnet)
Mailing address: Museum of Zoology, Univ. of Michigan, Ann Arbor, MI 48109
For further description see:

Eernisse, D. J. 1992. DNA Translator and Aligner: HyperCard utilities
    to aid phylogenetic analysis of molecules. CABIOS 8: 177-184.

The DNA Translator is a HyperCard 2.0 stack providing three complementary
sets of utilities for viewing and manipulating molecular data on a
Macintosh computer. First, DNA Translator displays codon and amino acid
usage data as it differs for a wide variety of organisms and organelles.
Dynamically-constructed graphs display percentage usage for a particular
codon relative to the other 63 codons or to only other codons with
equivalent amino acid coding. A user can select from a diverse list of some
70 taxon-organelle combinations. Second, a "gene mapping" facility draws
and displays 2 linearized gene maps for comparison, automatically
adjustable to desired scales and locations along all or part of the mapped
molecule. Maps and select corresponding complete sequence data are provided
for most available fully documented mitochondrial and chloroplast DNA
(mtDNA and cpDNA) sequences, which include 9 animal, 1 yeast, and 1 ciliate
mtDNAs and 3 green plant cpDNAs. Additional gene maps may be user-created
by a direct file conversion of standard GenBank- or EMBL-format documented
sequences and their features tables. Third, DNA Translator is a powerful
workbench of specialized sequence manipulation tools, catering especially
to those with interests in phylogenetic analysis. A user can extract the
sequence of any particular mapped gene or region by clicking on
the corresponding place on the gene map or by menu selection of the gene or
feature and mapped taxon. DNA Translator can also import single or
multiple sequences in a variety of formats, including multiple aligned
sequence output of various programs (EuGene, Prophet, CLUSTAL, Nexus,
PHYLIP, etc.), and then further manipulate, interleave, compare or
translate the gene sequences to amino acids. Multiple aligned sequences can
be converted to Nexus, Hennig86 or PHYLIP for subsequent phylogenetic
analysis. Most known deviations from the "universal" code, which are
typical for mtDNAs, may optionally be used during translation.
The codon usage, translation and gene mapping data may be exported or
imported in spreadsheet format for incorporating additional molecules of
interest or in various standard formats (UWGCG, GenBank,
EMBL,Intelligenetics). A built-in editor supports sequence entry with
optional computer-speaking for error checking, and a variety of output
conversion options. The current version is freely available via anonymous
ftp for noncommercial use only.

A.   Import Formats Accepted
   1.   Multiple sequence alignments
      a.   Simple text files of string sequences, with or without
           interleaves or match characters
      b.   MBIR (EuGene, Prophet) "Doolittle" progressive alignments
      c.   CLUSTAL nucleo- or peptide output.
      d.   Nexus (PAUP, MacClade) files
      e.   Phylip "Result" output files
   2.   String sequences
      a.   String sequence text files of the form: Name AGCTACCT...
      b.   Data input from built-in sequence entry editor
      c.   Sequences extracted from the provided gene mapper
      d.   String output generated by many commonly used programs
   3.   GenBank/EMBL or PIR-CODATA documented sequence files
      a.   Converted to string sequences for use in conversions below
      b.   GenBank or EMBL documented features to spreadsheet matrix
      c.   Matrix directly convertable to rescalable gene map
      d.   Gene map allows extraction of any mapped or custom subsequence
B. Conversions provided
   1.   Multiple sequence alignments (A1) converted/exported
        in the following formats:
      a.   Nexus (PAUP, MacClade) with optional cost matrices added
      b.   Hennig86 (Nucleotide data only)
      c.   Phylip 3.2 or 3.3 formats
      d.   Multiple sequence strings (A2a) with gaps preserved or deleted
   2.   String sequences (A2a,B1d) converted/exported in the
        following formats:
      a.   Unmodified to be reimported or converted as needed
      b.   As straight single sequence strings for import by MBIR
           (EuGene, Prophet), Authorin, Gene Construction Kit, etc.
      c.   Intelligenetics format for import by many programs
      d.   GenBank, EMBL, FASTP, or PIR-CODATA formats for viewing or
           import by many programs
      e.   Simple interleaved format with optional match characters
           for manual alignment or reimport (A1a)
      f.   Direct export of corresponding sequences (e.g., all animal
           mtDNA cyt. B genes) from gene mapping facility to Aligner stack
      g.   A subblock of aligned strings to MULFOLD (RNA folding) format
      h.   Consensus sequence created by combining two or more sequences
           employing ambiguous nucleotide symbols (IUPAC-IUB)
      i.   Subsequence, DNA <-> RNA,  upper <-> lower case, ACGTU -> 01233,
           filter IUPAC-IUB codes, complementary strand sequence conversions
      j.   Tally and display autapomorphies (site-unique nucleotides or gaps)
           for sets of aligned nucleotide strings
      k.   Compute compositional statistics of each nucleotide string
   3.   DNA/RNA -> peptide translation
      >   1st, 1st & 2nd, or all 3 possible reading frames output
      >   Formatted output displays codons below amino acid abbreviations
          with either 1- or 3-letter amino acid abbreviations
      >   String output is useful for export or conversion (B2)
      >   Can use standard or any of the provided codon usage tables
      >   Custom codon usage tables can be added using a table editor
      >   Codons with ambiguous nucleotide symbols (IUPAC-IUB) are
          translated as appropriate when translation is unambiguous
      >   Optional termination when stop codons are encountered
   4.   Peptide -> DNA translation
      >   Peptide strings can be backtranslated, using the reverse of
          whichever codon usage table the user selects
      >   Backtranslation uses IUPAC-IUB conventions for ambiguous
          nucleotides
D.   Nucleotide or peptide sequence entry
      >   Special Editor field has autoformatting capabilities
      >   Adjustable computer speaking supported during or after entry
      >   Sequences can be edited, manipulated, or exported (B2)
E.   Data provided with stack
      >   Codon usage patterns for about 70 organism/organelle combinations
      >   Most mitochondrial variation in coding supported (3)
      >   Gene maps of 11 mtDNAs plus string sequences
      >   Gene maps and matrices for 3 green plant chloroplast DNAs
F.   General Features
      >   Online help facility is available from any card in stack
      >   References, taxon names, and sample data provided
      >   Pulldown or popup menus or dialogs used for commands
      >   Buttons or pulldown menus are used for stack navigation
      >   Data fields can be locked or unlocked for text entry
      >   Data fields shrink down or expand by clicking
      >   Contents of fields exportable as text or printable
      >   Codon usage tables output for any incorporated taxon
      >   Gene maps and codon usage graphs have special printing options
      >   Default word processor for exported text files can be chosen
      >   PAUP/MacClade specification for exported Nexus files
      >   PAUP/MacClade open directly from the stack
      >   Add gene mapping or utility cards as required
      >   All data, scripts and resources used are easily accessible
      >   Custom XFCNs by Nigel Perry enable efficient manipulations
G.   Hardware and System Requirements
      >   Requires any Macintosh that can run HyperCard 2.0
      >   HyperCard 2.x (2.0 or 2.1) (Widely available for Macintosh users)
      >   Macintosh System 6.0.5 or greater (for HyperCard 2.0)
      >   2 or more MB Ram recommended
H.   Availability of current version
      >   Anonymous ftp to um.cc.umich.edu (35.1.1.43)
          After connection type 'cd gdef' and 'get dnastack.hqx'
          Resulting file needs to be "debinhexed"
          This will most likely be more current than the following
          due to more frequent updates.
      >   Anonymous ftp to at least the following site
          Ftp.Bio.Indiana.Edu (after connection: 'cd molbio/mac'
          and 'get DNASTACK.HQX')
      >   EMBL file server by sending the command:
          GET MAC_SOFTWARE:DNATRANSLATOR.HQX to [e-mail]
          Entire package is approximately 550K in binhexed form
      >  As of 9/24/91 includes Aligner stack described below

Aligner is a freeware HyperCard 2.x stack for manual alignment of
sequences by D. J. Eernisse, author of DNA Translator stack. Aligner was
inspired by a stack called MultiDNA by Ralph Gonzalez, but was created
completely from scratch. Enhancements compared to MultiDNA include: 1)
Number of sequences that can be aligned increased from 6 to 100; 2)
interleave formatting and number lines automatically adjust for the
number of sequences imported; 3) now accomodates sequences up to 30,000
bp or amino acid residues long; 4) imports or exports multiple sequences
that are simple return-delineated strings or in 'DNA Translator' stack
string format (i.e., 'Name<space>AGCTGA...<rtn>'); 5) optionally
interleaves exported sequences; 6) enlarged for use on a 640 x 480
standard color or larger monitor (automatically adjusts for standard
small Mac screens);  7) much faster switching between sequences to be
edited; 8) can toggle between match characters (dashes) to the first
sequence and no match characters; 9) speaks nucleotide/peptide
characters during keyboard entry or after entry starting from the
current insertion point; 10) various sequence manipulations, such as
lower <-> UPPER case; 11) can add/delete gaps to/from all but the
currently selected sequence; 12) align amino acids, then introduce gaps
to the corresponding unaligned nucleotide strings to preserve the
amino acid alignment; 13) custom menus; 14) several options to color
text in the alignment including a color coding of nucleotide triplets
according to their amino acid coding, with multiple alternate genetic
codes supported; 15) error checking routines for comparing the
nongap characters against your starting file; 16) import multiple
sequences for a particular gene directly from DNA Translator stack
gene mapping facility (e.g., all avaialable animal mtDNA sequences
encoding cyt B gene); 17) optional help facility displays the function
of fields or buttons as the cursor enters them.

This stack is distributed separately or as part of the more extensive
DNA Translator stack package. The best way to get the most current
version of either stack is via anonymous ftp to "um.cc.umich.edu) then
"cd gdef" and "get aligner.hqx" or "get dnastack.hqx" for Aligner stack
only or the entire package, respectively. Then debinhex the resulting files.
Aligner by itself is under 300 K uncompressed, while DNA Translator and
associated files occupy about 1 MB on your hard disk (500K in compressed
Binhex format).

This stack is only free for any noncommercial use and is not public
domain.  It is copyrighted 1991,1992 by D. J. Eernisse, and uses some XFCN
resources copyrighted by Nigel Perry with similar copyright restrictions
(see stack script for details). For more information, contact:

Douglas J. Eernisse Museum of Zoology, Univ. of Michigan, Ann
Arbor, MI 48109 USA [e-mail] or usergdef@umichum

For further information, tips, trouble-shooting, and version history,
see the online help facility.