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All,

and more...the March newsletter...

cheers 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 - March 2004
  ########################################

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>.

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This month sees a small extension to the EST read pair code and to the
output of confirmed introns in GFF format and some bug fixes.

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


      EST Read Pairs
      ++++++++++++++

As explained in the June 2002 newsletter
<http://www.acedb.org/winfo/Newsletters/Year2002/June.html#Homols_ESTs>
it's possible to have EST read pair homologies joined by dotted lines on
the FMap. This can be very helpful where there are lots of ESTs or pairs
are far apart making them difficult to spot.

This facility has been extended to allow ESTs that have different SMap'd
parents to be joined up, this has been useful for genomes such as Zebra
fish where the read pairs may be very far apart.

Note homologies are *_only_* shown with solid and dotted lines when you
show the column in "cluster" mode.


      Confirmed intron reporting in GFF output
      ++++++++++++++++++++++++++++++++++++++++

There has been some rationalisation of confirmed intron output in GFF.
The confirmations will now be reported in the format:

|<mandatory GFF fields> Sequence <parent_sequence_name> [Confirmed_XXX
[confirming_sequence_name] ;]

(XXX will be one of:  EST, cDNA, Homology, UTR, False or Inconsistent)
|

The Confirmed_XXX section will be repeated for all the confirmations for
that intron and may be followed by the name of a confirming sequence in
the database.

So for a sequence containing:

|Confirmed_intron         39403 40250 EST
Confirmed_intron         39403 40250 cDNA
Confirmed_intron         39403 40250 UTR
Confirmed_intron         39403 40250 Homology
|

the GFF record will be:

|B0454   curated intron  39403   40250   .       +       .       Sequence
"B0454.1" ; Confirmed_by_cDNA ; Confirmed_by_EST ; Confirmed_by_homology ;
Confirmed_in_UTR
|

If there are multiple confirming sequences for a confirmation type they
will all be output. So given:

|   EST  b0250
        b0250.1
        etc.
|

they will all be dumped as:

|    Confirmed_EST b0250 ; Confirmed_EST b0250.1 ; etc......
|

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


      Fix handling of ECONNRESET
      ++++++++++++++++++++++++++

Code in the socket library for the socket server did not handle
ECONNRESET properly (heppens when a client terminates without saying
goodbye), this is now fixed.


      CDS DNA dumping bug
      +++++++++++++++++++

Another bug caused by the move to having arbitrary classes SMap'd for
FMap. The code only allowed Sequence class objects with a CDS tag to
have their CDS DNA dumped, fixed now.

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    March 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: Tue Apr 13 18:30:31 BST 2004