
                                  abiview 



Function

   Display the trace in an ABI sequencer file

Description

   abiview reads in an ABI sequencer trace file and graphically displays
   the data. The probabilities of each of the 4 nucleotide bases along
   the sequencing run is plotted and the assigned nucleotide (G, A, T, C
   or N) from the ABI file is overlayed on the graphs. The complete
   sequence is written to an output file.

Usage

   Here is a sample session with abiview


% abiview -graph cps 
Display the trace in an ABI sequencer file
ABI sequencing trace file: abiview.abi
nucleotide output sequence [abiview.fasta]: 

Created abiview.ps

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infile]            infile     ABI sequencing trace file
  [-outseq]            seqout     [.] Nucleotide sequence
                                  filename and optional format (output USA)
   -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png, gif)

   Additional (Optional) qualifiers:
   -startbase          integer    [0] First base to report or display (Integer
                                  0 or more)
   -endbase            integer    [0] Last sequence base to report or display.
                                  If the default is set to zero then the
                                  value of this is taken as the maximum number
                                  of bases. (Any integer value)
   -yticks             boolean    [N] Display y-axis ticks
   -[no]sequence       boolean    [Y] Display the sequence on the graph
   -window             integer    [40] Sequence display window size (Any
                                  integer value)
   -bases              string     [GATC] Base graphs to be displayed (Any
                                  string is accepted, matching regular
                                  expression /[GATC]+/)

   Advanced (Unprompted) qualifiers:
   -separate           boolean    [N] Separate the trace graphs for the 4
                                  bases

   Associated qualifiers:

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   This reads in a standard ABI trace file.

  Input files for usage example

  File: abiview.abi

   This file contains non-printing characters and so cannot be displayed
   here.

  File: abiview.abi

   This file contains non-printing characters and so cannot be displayed
   here.

Output file format

   It outputs a file holding a normal nucleotide sequence.

  Output files for usage example

  File: abiview.fasta

>../../data/abiview.abi
GNNNNNNNNNGNGNNGGGGTTTNANNNTNNNAGAACCCCCCTTNGAAAANNNCCACCCCA
NNATAGTNGTANGAATAGTNCCCAGGCCANGCCTATCTGTGATGATTACATAGGCTAACA
CATGACAAACATTTAAAAACACTAAACAATTGTTATTTATTCTTTGTTCCTATAAACCAC
ACCCATTAAGCCCTTACTATATATAAGAGTTTTCAAGCCAAGAACCTGCTGCTTGGGAGG
CTGATGCAGGAGAATTGCCAAGTACAAACCCTGCCTGGACTGTAAAGTGAAACCAAGGCT
AGTTGTCTCACAATAAAAGATGAAGGGCAAGTGGGATCAATGCATAAAGGAGCTTGTGCC
CAAGCCTGTTAGCCTTAGTTCAATTCCTGAGTACCATGAAAAGGTAGAAGGAGAGAAATG
ATTTGGTACAATTTTTCTCTGTGCTGTGACACAGTACCACCCTCCTACTAATAACAAATA
AAATAATGTTTAAAACAAAATAAAATAAAAATGGACTGGGATGTAGCACAATGGTAGGGT
ACTTGCATAGCATGTACAAGGACCTGATTTCAATCCCCTGTGATAAAAGAAAATAAGGAA
GGGAGGAAGCGTTAGGAGGAAAAATGGAATACAGAAGACACAGTGCATGGGAAGGATATG
TATGTTATGAACACCAGAAATTCACTTGAAAATGAGTAAAATTTTTTTATTATTATATCA
TTATTATTGGGGGGGATGTGGGCGGGGCTTGCAGAGGTATCTTTTAGAGGANGATCATTT
TCCGGTTGTTGAGCAGGGCTCTGTTATGTAGGATATCTCAGANTAACAGACCCCAGGT

  Graphics File: abiview.ps

   [abiview results]

   The horizontal scale of the output image labelled 'Residue Position'
   is only a very approximate indication of the spacing of residues in
   the image. The real residue spacing is variable, as it relies on the
   speed with which the oligo-nucleotides are eluted in the ABI
   sequencer. Do not be surprised to see the nucleotide signals spaced at
   a much greater distance than the horizontal scale might suggest.

Data files

   None.

Notes

   An ABI file (*.abi) contains sequence trace data and base calls from a
   run of an ABI nucleotide sequencer machine. A trace data file is what
   you get back from having some DNA sequenced, for example, by a 3730XL
   sequencer. The files are in "binary" format and so cannot be viewed
   directly on screen. To inspect the sequencing data you must use a
   trace viewer such as abiview. Another good trace viewer is FinchTV
   (http://www.geospiza.com/finchtv/). It is stand-alone program and is
   freely available.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name Description
   cirdna Draws circular maps of DNA constructs
   lindna Draws linear maps of DNA constructs
   pepnet Draw a helical net for a protein sequence
   pepwheel Draw a helical wheel diagram for a protein sequence
   prettyplot Draw a sequence alignment with pretty formatting
   prettyseq Write a nucleotide sequence and its translation to file
   remap Display restriction enzyme binding sites in a nucleotide
   sequence
   seealso Finds programs with similar function to a specified program
   showalign Display a multiple sequence alignment in pretty format
   showdb Displays information on configured databases
   showfeat Display features of a sequence in pretty format
   showseq Displays sequences with features in pretty format
   sixpack Display a DNA sequence with 6-frame translation and ORFs
   textsearch Search the textual description of sequence(s)

Author(s)

   Tim Carver (tcarver © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Written (January 2001) - Tim Carver

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
