Fw: Other: EMBOSS versus GCG?

[Peter Rice]

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