Fw: Other: EMBOSS versus GCG?

Gary Williams, Tel 01223 494522 gwilliam at hgmp.mrc.ac.uk
Fri Nov 15 14:35:35 UTC 2002

I started to produce some code for a feature plot, but got bogged down
in graphics and have been waiting for the new graphics libraries to
appear before continuing.

If anyone wants to look at what I have already, I can mail it to them.

I would like it to output a graphics image and a file that could be used
as an HTML client-side or server-side image active area map.


Peter Rice wrote:
> Rory Bowden wrote:
> > This on the 'evoldir' list, which is the main international mailing list in
> > evolutionary biology. Would anyone like to make any comments for me to pass
> > on?
> >>  It is my impression
> >>that GCG is in a different league. For example, compare the GCG program
> >>"Window" with its proposed EMBOSS alternative "Freak":
> >>
> >>TASK: Determination of the number of occurences of a motif in a sequence
> >>window.
> >>
> >>GGC program WINDOW
> >>
> >>1. Allows up to 6 motifs at a time
> >>2. Outputs absolute values and has a variety of other output options.
> >>3. Extensive input menu
> >>
> >>EMBOSS program FREAK
> >>
> >>1. Allows only 1 motif at a time.
> >>2. Outputs a calculated fraction.
> >>3. Very limited input menu.
> Window : produces scores over a 'window' (a base range).
> StatPlot : Plots Window results
> EMBOSS : reports have scores over a base range as a general output format.
> Freak: frequency of matches
> FuzzNuc/FuzzPro/FuzzTran: Pattern matches with ambiguity codes
> Restrict: Pattern matches with a pattern file
> etc...
> This makes it possible to develop some really nice new EMBOSS applications.
> So ... how about a program  which reads EMBOSS report files and produces a
> summary report (think of window), and another that plots them all (think of
> statplot). Scores could be plotted if we have a good way to compare them.
> Yes, I know freak does not produce a report file ... but that is a very
> easy change.
> It could also read in EMBL/SwissProt feature tables as annotation.
> So, suggestions please for EMBOSS applications to plot reports/features...
> For example:
> 1. xy plot of scores as points at the centre of a feature, with the
> sequence position on the x axis and the score on the y axis. Possibly split
> into multiple plots by program/feature-type/named-tag-value (e.g. pattern)
> (like statplot only much more versatile).
> 2. xy plot of lines for each feature
> 3. GANTT (bar) chart of features by position, annotated with feature
> type/program/score as appropriate
> 4. Combine these - xy plot of features with scores, and other features
> reported underneath (think of the -mark option in statplot - but with far
> more annotation possible below the x axis)
> Maybe we can make some mock-ups on the EMBOSS pages to show the possibilities?
> regards,
> Peter
> --
> ------------------------------------------------
> Peter Rice, LION Bioscience Ltd, Cambridge, UK
> peter.rice at uk.lionbioscience.com +44 1223 224723

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

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