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UnderConstruction Under Construction...

PROGRAM DESCRIPTION

aplot - Pair-wise Alignment-Plots for Genomic Sequences in PostScript.

Our basic goal is to provide an easy-to-use filter to get plots that will be useful in genomic analysis, and also giving enough quality to include them into your documents without losing resolution. We defined a simple format from GFF format to define pair-wise alignments, but now program can also read standard GFF for those alignments too.

`General Finding Format' (GFF) is described on the Sanger Centre gff definition page.

EXAMPLES

UnderConstruction        Following this link you can get some snapshots of aplot output.

NEWS

26 Jan 2000  v1.9  After several bug fixes and versions not published, here is the new version for aplot.
This version can work with "partial" custom files (without having to define all the variables) and can also read alignments in standard GFF format:
    <seq_name> <source> <feature> <startX> <endX> <gapped_align_score> <strand> <frame> ...
     ... <Target "group_name"> <startY> <endY>; <optional_tag> <global_align_score>
24 Apr 1999  v1.3  Defaults are defined within the main gawk script too. Thus custom file is not mandatory now.
22 Mar 1999  v1.2  Zoom option was defined. Data vectors can be passed to plot functions on the third panel.
02 Mar 1999  v1.0  First running version for aplot.
Annotation on axes is defined in GFF-format.
Alignment definition is written in pseudo GFF:
    <seq_nameX:seq_nameY> <source> <feature> <startX:startY> <endX:endY> <gapped_align_score> ...
     ... <strand> <frame> <global_align_score:group>

DOWNLOADING

Download last version of aplot (v1.9) from our ftp server.

You can find there a gzipped tarball containing the Scripts, a README text file and few example drawings.

Once you have downloaded files, you can extract them with:

`*.gz' gunzip *.gz
`*.tar.gz' gunzip -c *.tar.gz | tar xvf -
On Linux you can try with:   tar zxvf *.tar.gz

WEB SERVER

UC aplot server is under construction.

Thanks to Vadim Goremykin from IMB at Jena (Germany), who is writing the scripts for the aplot web server. When it will be finished we should install a mirror in our server...

FEATURE LIST

This menu shows many features of aplot.

  • Plot attributes are set from a custom file that is created by default first time you use aplot, which contains all variable names in a readable list of name-value pairs.
  • Now is possible to define an extra customization file_name to be included within variables and attributes definition.
  • Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement.
  • Sub-alignment scores can be visualized in a PiP box below aplot area, also with grey_scale, color or width gradients (score dependent).
  • Extra panel at page bottom where you can display any feature or functions related with X-axes sequence.
  • Scalable fonts and rotation angle for feature and group labels.

    • TO DO LIST

    Although we have implemented many features, there are some ideas to be added before releasing version 2.0 of aplot.
    Here is a short list:

  • Draw different alignments on same aplot with different colors.
  • Display alignment strand and frame.
  • Make custom file like the one being used in gff2ps.
  • Include gff2ps format in extra-box.
  • gff2ps shape dictionary will be imported to aplot.
  • Crossing ribbons will mix their colors.

    • We thanks any helpful suggestion for improving our program. Message should contain "APLOT - SUGGESTION" as subject string.

    REPORTING BUGS

    If you find any bug or something is not plotted properly, you can send a bug report that should contain as subject string: "APLOT - BUG REPORT". To easily find what's wrong, you should attach to that e-mail a tarball containing the custom file you were using when the bug ocurred, an example of your input GFF files, the PostScript file generated and a report file that you can get from the standard error with the "-V" command-line option. We will try to answer as soon as possible.

    AUTHORS

    Josep Francesc ABRIL FERRANDO
    Thomas WIEHE
    Roderic GUIGÓ SERRA

    CopyRight © 1999

    aplot is under GNU General Public License.

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