[ssml] Multiple Alignment to PSSM

[Yun He]

Hi, Rajesh

I had asked the same question here several months ago, some one told me that 
it is very difficult to covert the alignments into PSSM in the manner of 
BLAST/PSI-BLAST, but you can do that with HMMER instead. Then I tried to use 
HMMER, yes, HMMER really can. 

/usr/local/HMMER/bin/hmmbuild -F --fast --gapmax 1 --wblosum tmp.hmm 
your_multialignments_in_FASTA_format.fasta > /dev/null
/usr/local/HMMER/bin/hmmconvert -F -p tmp.hmm profile_in_HMMER_format.prof 
> /dev/null

If you want to convert profile_in_HMMER_format into PSSM format, can use this 
Perl script:

##Main part
my @effective_alphabet = qw(A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  
W  Y  V);	## Columns order like PSSM

my $normalized_ratio = 100; ## set this if you want to normalize those columns

my @hmmprof;
	&read_hmmprof("profile_in_HMMER_format.prof", \@hmmprof);

      print "  ";
	for(my $i=0; $i < scalar @effective_alphabet; $i++)
	{
		printf "    %s   ", $effective_alphabet[$i];
	}
	print "\n";
	
	for(my $i=0; $i < scalar @hmmprof; $i++)
	{
		printf "%1s ", substr($your_query_sequence, $i, 1);
		for(my $j=0; $j < scalar @{$hmmprof[$i]}; $j++)
		{
			printf "%7.3f ", $hmmprof[$i][$j]/$normalized_ratio;
		}
		print "\n";
	}

exit 0 ;

sub read_hmmprof
{
	my $file = shift;  ## INPUT: HMM profile format
	my $prof = shift;  ## OUTPUT: ref of array (profile matrix)
	
	open IN, $file or return 0;
	my $c = 0;
	my @matrix;
	my @order;
	while (<IN>){
	if (/^Cons/){
	@order = (split / +/)[1..24]; 
		while (($line = <IN>)!~ /\*/)
		{				
			if ($line !~ /\!/){
				@{$matrix[$c]} = (split / +/, $line)[2..25];
				$c++;
			}
		}
	}
	}	
	close IN;
	
	my @idxorder;
	for(my $i=0; $i < scalar @effective_alphabet; $i++){
		for(my $j=0; $j < scalar @order; $j++){
			if($effective_alphabet[$i] eq $order[$j]){
			$idxorder[$i] = $j;
			last ;
			}
		}
	}

	for(my $i=0; $i < scalar @matrix; $i++)
	{
		for(my $j=0; $j < scalar @effective_alphabet; $j++)
		{
			$prof->[$i][$j] = $matrix[$i][$idxorder[$j]];
		}
	}
	undef @matrix;
	return 1;
}

=== Jarod

On Saturday 30 April 2005 00:07, ssml-general-request at bioinformatics.org 
wrote:
> Dear All,
>
> I have a set of multiple alignments which I want to convert into PSSM
> profiles (searchable byr RPSblast). Could anyone please tell how to achieve
> this?
>
> Thanks in advance.
>
> Rajesh
>
>
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