🚀 go-pugleaf

All,

By popular demand (ok, ok, not exactly popular demand), I have reinstated the
newsletter. It turned out (inevitably) that we are still needing to make changes
and upgrades to Acedb (of course), so while the newsletter will be terse, it
will still be worth something...I hope.

Please find below, Decembers newsletter, Novembers will on the web site by
tomorrow.

Ed
-- 
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| Ed Griffiths, Acedb development, Informatics Group,                    |
|        Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,  |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif@sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |
 ------------------------------------------------------------------------



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  ACEDB User Group Newsletter - December 2003
  ###########################################

If you want to have this newsletter mailed to you *_or_* you want to
make comments/suggestions about the format/content then send an email to
acedb@sanger.ac.uk <mailto:acedb@sanger.ac.uk>.

------------------------------------------------------------------------

This month sees better support for Confirmed Introns in FMap, some
changes to EMBL dumping to better support SMap'd classes, some
improvements to GFF output and yes, the usual bug fixes.

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    New Features
    ************


      Confirmed Introns in FMap
      +++++++++++++++++++++++++

If you click on a Confirmed Intron in FMap you will now see which
sequence(s) confirms that intron in the blue report line at the top of
FMap.

------------------------------------------------------------------------


    Articles
    ********


      EMBL dumping
      ++++++++++++

If you don't use the EMBL dumping options from AceDB then you don't
really need to read this.

Changes to the wormbase database models have enforced some changes to
the EMBL dumping routines in AceDB, this will almost certainly affect
you if you use the AceDB EMBL dump routines.

Only objects that specify an EMBL_dump_method via the EMBL_dump_XXXX
tags will now get dumped, otherwise they will be ignored, this is a
tightening up on previous behaviour.

The code now knows how to handle the new Wormbase CDS_child, Transcript,
Pseudogene and Transposon classes. The Pseudogene tag has changed to
either Coding_pseudogene or RNA_pseudogene. This has required small but
significant changes to the code that handles CDS vs. RNA and whether
something is a pseudogene. If you make use of these tags you should try
out the EMBL dump routines before submitting data to EMBL.


      More FMap/SMap/GFF changes
      ++++++++++++++++++++++++++

We have added a new FEATURE_OBJ seg type for more generalised features
that result from smap objects that are not Sequence class objects. These
new segs can be handled in a more generalised way than before.


      GFF changes
      +++++++++++

GFF dumping has been improved so that parent/child related features are
dumped properly, i.e. a CDS with is relevant exons/introns is now
labelled correctly. This includes better support for the GFF_XXX tags in
the Method class.

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    Bugs Fixed
    **********


      Confirmed Intron bug
      ++++++++++++++++++++

A stupid bug in setting the position of confirmed introns meant that in
certain circumstances they could be off by one on the forward strand and
off by two on the reverse. The basic cause of the bug was forgetting
that database coords are 1-based but FMap segs are 0-based.


      SMap bug
      ++++++++

Fixing a bug in blixem whereby % identity was not correctly calculated
for gapped alignments revealed a bug in sMapLocalMapEx() which caused
the nucleic acid coords for a protein alignment to be truncated.


      Blixem bug
      ++++++++++

Fixed a number of problems with blixem:

    * Very long sequence names are now abbreviated in the middle so
      annotators can still see beginning/end, current abbrev. is "><".
    * The selected sequence name was being truncated, this is no longer so.
    * The % identity routine did not do gapped alignments, it does now
      but not for tblastn or tblastx which will need further work.

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    Developers Corner
    *****************


      ZMap
      ++++

December has seen much work to get our systems into a state where we can
get on with the detailed implementation of ZMap, we've decided to use
more of the Gnome/GTK software as it is widely ported and most readily
available on Linux.

We've decide for instance to make use the Gnome Canvas for drawing the
sequence etc. as this provides many useful features including complete
support for event handling based on what in the Graph package would be
"boxes".


      classModel2Class() function
      +++++++++++++++++++++++++++

Added classModel2Class() function that given the key that equates to
"?>model<" (e.g. "?Sequence"), as found in the model for a class,
returns the int that represents that class, returns 0 on failure. This
slightly odd looking function is useful when writing code that needs to
trawl through the models for a number of classes, see code in
w7/fmapgene.c which needs to dynamically examine the database models and
record which classes contain certain tags.


      Aquila changes
      ++++++++++++++

Rob Clack has been making more changes to our build/test system to
further improve its automation and save us work in the future. He has
also fixed a number of problems as Sanger systems have migrated to new
levels of Linux, OSF etc.

------------------------------------------------------------------------


    December monthly build now available.
    *************************************

You can pick up the monthly builds from:

*Sanger users*
    ~acedb/RELEASE.DEVELOPMENT
*External users*
    http://www.acedb.org/Software/Downloads/monthly.shtml
    <http://www.acedb.org/Software/Downloads/monthly.shtml>

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Ed Griffiths <edgrif@sanger.ac.uk> <mailto:edgrif@sanger.ac.uk>

Last modified: Thu Jan 8 13:30:40 GMT 2004