Fw: Other: EMBOSS versus GCG?
peter.rice at uk.lionbioscience.com
Fri Nov 15 13:20:13 UTC 2002
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
>> 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
>>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
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
It could also read in EMBL/SwissProt feature tables as annotation.
So, suggestions please for EMBOSS applications to plot reports/features...
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?
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723
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