[Bioperl-l] Recovering conservation lines from clustalw

[Peter Schattner]

Hello Josep

I'm a little puzzled by your query.

Josep Francesc Abril Ferrando wrote:

>
> At this moment I am parsing a clustalw alignment using Bio::UnivAln, with the variables properly set
> to use clustalw for parsing the input files. I can recover each sequence and its identifiers from a
> single alignment, I can obtain the consensus sequence, and so on. The problem is that I will need
> also the conservation line that appears below each alignment (that one containing only '.', ':' and
> '*'). Is there any method defined to recover such lines ?

 UnivAln.pm can directly read only fasta and "raw" data formats.  AlignIO.pm does read and write
clustalw format .  However it does not read or write a "conservation line" appearing below each
alignment.  In fact in the - admittedly not very many - clustal alignment files I've seen, I don't
think I've  seen a conservation line.  If you send in an example clustal file which includes
conservation lines, we can take a look at them and (assuming they are a standard clustal format)
possibly include parsing them with  AlignIO.  However, at the moment I'm pretty sure bioperl doesn't
support this capability.

Regards

Peter Schattner