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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.
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.
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......
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.
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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