EMBOSS: abiview


Program abiview

Function

Reads ABI file and display the trace

Description

abiview reads in an ABI sequence trace file and graphically displays the results.

The data for each nucleotide is plotted and the assigned nucleotide (G, A, T, C or N) in the ABI file is overlayed on the graphs.

It also writes out the sequence to an output sequence file.

Usage

Here is a sample session with abiview:

% abiview
Name of the ABI trace file: ba16d2.s1
Output sequence [outfile.fasta]: 
Graph type [x11]: 

Command line arguments

   Mandatory qualifiers:
  [-fname]             string     Name of the ABI trace file
  [-outseq]            seqout     Sequence file
   -graph              xygraph    Graph type

   Optional qualifiers:
   -yticks             bool       Display y-axis ticks
   -[no]sequence       bool       Display the sequence on the graph
   -window             integer    Sequence display window size
   -bases              string     Base graphs to be displayed

   Advanced qualifiers:
   -separate           bool       Separate the trace graphs for the 4 bases

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-fname]
(Parameter 1)
Name of the ABI trace file Any string is accepted An empty string is accepted
[-outseq]
(Parameter 2)
Sequence file Writeable sequence <sequence>.format
-graph Graph type EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png EMBOSS_GRAPHICS value, or x11
Optional qualifiers Allowed values Default
-yticks Display y-axis ticks Yes/No No
-[no]sequence Display the sequence on the graph Yes/No Yes
-window Sequence display window size Any integer value 40
-bases Base graphs to be displayed Any string is accepted GATC
Advanced qualifiers Allowed values Default
-separate Separate the trace graphs for the 4 bases Yes/No No

Input file format

This reads in a standard ABI trace file.

Output file format

It outputs a file holding a normal nucleotide sequence.

It outputs a graphical image of the traces.
The graphical output from the above example is here.

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

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
cirdnaDraws circular maps of DNA constructs
lindnaDraws linear maps of DNA constructs
pepnetDisplays proteins as a helical net
pepwheelShows protein sequences as helices
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
seealsoFinds programs sharing group names
showalignDisplays a multiple sequence alignment
showdbDisplays information on the currently available databases
showfeatShow features of a sequence
showseqDisplay a sequence with features, translation etc
textsearchSearch sequence documentation text. SRS and Entrez are faster!

Author(s)

This application was written by Tim Carver (tcarver@hgmp.mrc.ac.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.

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