|
|
EMBOSS: abiview |
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.
% abiview Name of the ABI trace file: ba16d2.s1 Output sequence [outfile.fasta]: Graph type [x11]:
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 |
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.
| Program name | Description |
|---|---|
| cirdna | Draws circular maps of DNA constructs |
| lindna | Draws linear maps of DNA constructs |
| pepnet | Displays proteins as a helical net |
| pepwheel | Shows protein sequences as helices |
| prettyplot | Displays aligned sequences, with colouring and boxing |
| prettyseq | Output sequence with translated ranges |
| remap | Display a sequence with restriction cut sites, translation etc |
| seealso | Finds programs sharing group names |
| showalign | Displays a multiple sequence alignment |
| showdb | Displays information on the currently available databases |
| showfeat | Show features of a sequence |
| showseq | Display a sequence with features, translation etc |
| textsearch | Search sequence documentation text. SRS and Entrez are faster! |
