# ACEDB User Group Newsletter - March 2004

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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.

## New Features

### EST Read Pairs

As explained in the June 2002 newsletter 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......

## 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.

## 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

Last modified: Tue Apr 13 18:30:31 BST 2004