[Bioperl-l] the roundup (long)

[Steve Chervitz]

On Thursday, Aug 14, 2003, at 05:33 US/Pacific, Jason Stajich wrote:

> I've added a bunch of new things and fixed some bugs, wanted to try and
> summarize before I get too busy and forget the details.

Good on you, Jason.

> [Bio::SearchIO]
>
> Additionally a SearchIO::blasttable has been added which can parse 
> NCBI -m
> 8 or -m 9 output for those just needing some minimal information.

Just the other week, I was thinking that Bioperl needs this. Glad to 
see you've already done it. Parsing speed and memory usage should be 
improved, eh?

Speaking of blast table parsing, it would really be useful if the NCBI 
blast tabular output included the length of the hit and query 
sequences. This would enable the frac_aligned methods of the Hit and 
HSP objects to work. Being able to determine the percent of the hit and 
query that are aligned is often vital.

I recently mentioned this to a member of the NCBI blast development 
team (Tom Madden) and he seemed pretty receptive to putting this in. 
Don't know what the timeframe would be.

Steve