I am converting outputs in stockholm format to clustalw using
Bio::AlignIO->new(-file => "$ARGV[0]", -format => "stockholm"); and
Bio::AlignIO ->new (-format =>'clustalw');
I am also using
my $new=$aln->remove_columns(['all_gaps_columns'],'.');
and got an output like
head1 ----------------.GG-.-gggaguggugugguuacgaaugUGGCCUCUGC-----A
head2 GGGGGUGUAGCUCAGU.GGU.A......................GAGCGGAUGCUUUGCA
What is the meaning of dots and dashes? Is this natural in a clustalw output? Am I getting a bug?
I was unable to find the sequences I used in the original message but these two pose a similar pattern. These are RNA sequences, including pseudogenes, so there are lots of palindromic sequences.
# STOCKHOLM 1.0
#=GF AU Infernal 1.1.1
head1 --------UGGAGAAU.G--.-ugggcguc.gaucccacUUCCUCUCGCAUGCUAA..............................................................GCGAGC-gcucuaccacuugagcuaauucccc-..-------------..................................
#=GR head1 PP ........89999988.4....6789****.********999**************..............................................................******.7999999866665555555554444..................................................
head2 --------UGGAGAAU.---.-gcgggcaucgaucccgcUUCCUCUCGCAUGCUAA..............................................................GCGAGCG.........................-..-------------cucuaccauu........................
#=GR head2 PP ........89999887......46789************9999*************..............................................................*****86.........................................4555666666........................
CLUSTAL W (1.81) multiple sequence alignment
head1 --------UGGAGAAU.G--.-ugggcguc.gaucccacUUCCUCUCGCAUGCUAA....
head2 --------UGGAGAAU.---.-gcgggcaucgaucccgcUUCCUCUCGCAUGCUAA....