[Bioperl-l] parsing output from an avid alignment

[Shawn Hoon]

Using bioperl-run
you could try using mlagan Bio::Tools::Run::Alignment::Lagan
for alignment as well. There are wrappers for it that generate 
SimpleAlign objects.
Then you could use Bio::Tools::Run::Vista
which takes in a SimpleAlign object and generates the vista plots.

The Vista wrapper actually converts the align object into a binary form 
of the AVID output
which makes Vista run faster.

shawn

On Jun 8, 2004, at 3:39 AM, Jonathan Manning wrote:

> Hi all,
>
> I'm preparing to incorporate Vista analysis into my script, and am
> attempting to use the AVID global alignment algorithm, since they seem
> to be associated, and likely to work well together.
>
> I don't think there is, but just in case I've missed something, has
> anyone written a module to parse the AVID output? Apparently it's a
> hybrid of the fasta and ClustalW styles. Here's an excerpt of the kind
> of thing I mean:
>
> 1419  t   |
> 1420  c   |
> 1421  a   |
> 1422  a   |
> 1423  t   |
> 1424  a   |
> 1425  g   |
> 1426  g   |
> 1427  t   |
> 1428  g - g  9
> 1429  a - a  10
> 1430  c - c  11
> 1431  t - t  12
> 1432  a   g  13
> 1433  a - a  14
> 1434  a - a  15
> 1435  a   g  16
> 1436  g - g  17
> 1437  t   |
> 1438  c   |
> 1439  t   |
> 1440  c   |
> 1441  t   |
> 1442  a   |
> 1443  a   |
> 1444  a   |
> 1445  g   |
>
> Cheers,
>
> Jon
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l