[Bioperl-l] An update for my DNA Smith-Waterman code

[Yee Man]

> 
> What errors are you getting?  We don't typically develop on SPARC (Sun,
> DEC, Linux, Win*, and Mac OS X are the primary environments).
> 

Never mind. Got it compiled now.

> Look for papers by Pearson and Miller.
> 

Thanks a lot.

> 
> No; many have asked us to put this code into a linkable library, but since
> this doesn't further our own research interests it's difficult to invest
> the necessary time.  We'd be happy to help anyone who wished to pursue
> this, though ... the "code-paths" you want to follow in dropgsw.c are
> "do_work" (calculate the score only), and "do_walign" (calculate the
> entire alignment).
> 

I will try to do this by myself then.

> 
> No, it allows the algorithm to run using vector datatypes so that
> calculating the DP matrix can be done in parallel.  But the FASTA programs
> all have threaded versions, as well as PVM and MPI runmodes.
> 

It will be great if you can send me paper/doc plus code. :)


> > I tried it but it seems to me ssearch34 only display the score only. How
> > can I get the alignment? How can I set gap penalty? I read the
> > accompanied fasta3x.doc but I still can't figure it out...
> 
> Make sure you are using a recent (version 3.4) distribution.
> 
> % ssearch34 -n -q -H -d 0 -b 1 t1.fa t2.fa

Finally get it running but I have to use my own scoring

ssearch34 -n -q -H -d 1 -b 1 -m 0 -f 3 -g 1 -r +3/-1 t1.fa t2.fa

This takes 50 sec in my machine but it is still faster than my fastest
implmentation (1 min 3 sec). However, if I use the default scoring, it
gives me the E() error and refuse to align. :(

Ewan: If licensing is not an issue, I can do the job of merging SWAT to
bioperl.

Thanks a lot
Yee Man