[Bioperl-l] few questions on TFBS

gtg974p at mail.gatech.edu gtg974p at mail.gatech.edu
Tue Jun 8 11:50:15 EDT 2004

Hi all,
I have few question while using TFBS perl modules with transfac.

1) while searching for TFBS using seq_search

my $seq = Bio::DB::GenBank->new()->get_Seq_by_acc('AF100993');
my $db = TFBS::DB::TRANSFAC->connect(-accept_conditions => 1);
my $pwm = $db->get_Matrix_by_ID('V$NGFIC_01','PWM');
my $siteset = $pwm->search_seq(-seqobj=>$seq, -threshold=>"80%");

For few matrices (like the one above) I am getting an error - "Can't call 
method 'seq_search' on an undefined value". Its working fine for the other 
matrices except a few(to name a few I$DFD_01, F$ABF_C,V$AP1_c..). The only 
similarity between all these matrices is they have integer values (instead of 
the raw counts). Either they are normalised to 4 or 100 or they are derived 
using consindex. I would greatly appreciate any suggestions to point me in the 
right direction. 

2) Is there any way to specify the background distribution for calculating PWM?


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