solved: Re: [Bioperl-l] Bio::Tools::Run::RemoteBlast not getting all hits

[Dan Kortschak]

Resolution: Bio::Tools::Run::RemoteBlast was working flawlessly.

During the move to the new machine a number of files (the problem ESTs
included) were not moved, and were subsequently not included in the
analysis. This seems to have been a result of a consistent file name
system not being implemented by the sequencing firm (does anyone want to
write a Bio::Human::ReliableLabWorker class?). The disparities between the
manual and automated blasts came from different files being available to
different people (I will be so happy when we get out unified db together).

anyway thanks all for the help
Dan

BTW what version of Bio::DB::GenPept is not broken by the new NCBI Entrez
(1.0 seems to be eg:
-------------------- WARNING ---------------------
MSG: unexpected location line
[href=//www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=20537335&itemID=7&view=gpwithparts>gene</a>
1..1017] in reading EMBL/GenBank/SwissProt, ignoring feature <a
(seqid=TRL3_HUMAN)
---------------------------------------------------
)

On Mon, 23 Sep 2002, Jason Stajich wrote:

> Dan - Did you blast these sequences by hand at ncbi and see what you get?
> i.e. did anything popping out as strange in those that are repeatably
> failing (like 0 hits)?
>
> Mat Wiepert has recently worked with the Tools::Run::RemoteBlast some
> more, perhaps we/he/you can try running one of the offending ESTs through
> with the latest code and see if things are clearer?
>
> Alternatively you could try running those offending ones through the
> netblast (blastcl3) that NCBI provides and post process them with a
> script (small problems with bioperl parser and the netblast output but
> it is manageable I think).  Hacky, but might get your dataset faster.
>
> -jason

-- 
_____________________________________________________________   .`.`o
                                                         o| ,\__ `./`r
  Dan Kortschak    kortschak@rsbs.anu.spanner.edu.au     <\/    \_O> O
                                                          "|`...'.\
  Before you criticise a man, try to walk a mile in his    `      :\
  shoes. Then, if he doesn't like what you have to say,           : \
  you'll be a mile away, and you'll have his shoes.               :  \

  The address above will not work, remove the spanner from the works.

By replying to this email you implicitly accept that your response may
be forwarded to other recipients.
Permission is granted for fair use reproduction.