[ssml] error from BLASTCLUST

[Manoj Tyagi]

Hello
      I have subscribed to the list as asked by you.
Well I looked at your reply but if you read the documentation of BLASTCLUST it 
says low complexity filtering is "off" by default. Now if this feature is off 
then why we get error. 

Plus if some one wants to active above feature how you could do that because in 
program options there is no option for low complexity. there was -F but i 
didn't understand what it is. 

regards,
Manoj 
Quoting Dan Bolser <dmb at mrc-dunn.cam.ac.uk>:

> 
> 
> 
http://www.dur.ac.uk/biological.sciences/Bioinformatics/blast_FAQs.html#BLASTSet
UpSearch
> 
> This is a simple problem that is often encountered when beginning to use
> blastclust.
> 
> The problem comes when blastclust uses low complexity sequence filtering
> by default, and the sequence it creates on the fly (which you may never
> actually see) is totally 'screened' by the filter. i.e. the whole sequence
> is replaced by X's.
> 
> This prevents anything useful being done with the sequence and leads to
> the error seen (I am not sure of the exact process that leads to the
> error in these cases).
> 
> The short answer is you can safely ignore these problems, or you can
> switch off low complexity filtering at the risk of a few seemingly
> significant matches (matches over low complexity regions are probably not
> as unlikely as the random sequence approximation makes them seem). 
> 
> Sorry that isn't a very clear description... 
> 
> The best thing to do is understand low complexity sequences (very simple
> sequence repeats) and why / how those are filtered. 
> 
> The standard program is repetitive (for low complexity), and DUST removes
> coiled-coil sequences (which can be highly repetitive).
> 
> A random sequence is maximally complex. A continious repeat of one
> character is minimally complex.
> 
> Cheers,
> Dan.
> 
> 
> On Thu, 2 Sep 2004, Manoj Tyagi wrote:
> 
> >Hello,
> >
> >Thanks for the reply to my BLAST query. 
> >
> >This time I have another query about BLASTCLUST which I am trying to use to
> 
> >clsuter my dataset. In the documentation it says by default it uses BLOSUM62
> 
> >with gap penalities etc. 
> >Now I want to use default options so I just simply give my dataset as input
> 
> >file & give output file names. 
> >
> >Problem is it throws warning & error saying 
> >"[NULL_Caption] WARNING: SetUpBlastSearch failed.
> >[NULL_Caption] ERROR: BLASTSetUpSearch: Unable to calculate Karlin-Altschul
> para
> >ms, check query sequence"
> >
> >it means it didn't find lamda & K values in precomputed tables so giving 
> >warning & errors. normally it should be there anyway I can provide that
> values, 
> >the question is HOW? in BLASTCLUST there is no option for providing these 
> >values. 
> >
> >Could you help me out, what to do in this case. & why it is giving error? 
> >
> >regards,
> >Manoj
> >Quoting Kevin Karplus <karplus at soe.ucsc.edu>:
> >
> >> The matrix is not the whole set of parameterization for BLAST.
> >> There are also the gap costs and the lambda and K values used for
> >> computing E-values.
> >> 
> >> Changing the matrix without correcting the other parameters leads to
> >> uninterpretable results.
> >> 
> >> Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
> >> Senior member, IEEE	Board of Directors, ISCB (starting Jan 2005)
> >> Professor of Biomolecular Engineering, University of California, Santa
> Cruz
> >> Undergraduate and Graduate Director, Bioinformatics
> >> Affiliations for identification only.
> >> 
> >
> >
> >**********************************************************************
> > Manoj TYAGI 
> > Laboratoire de Biochimie et Génétique Moléculaire
> > Université de La Réunion
> > BP 7151, 15 avenue René Cassin
> > 97715 Saint Denis Messag Cedex 09
> > La Réunion
> > FRANCE
> > Tel : +262 262 938641
> > Fax : +262 262 938237
> >**********************************************************************
> >
> >
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> >ssml-general at bioinformatics.org
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> >
> 
> 
> 


**********************************************************************
 Manoj TYAGI 
 Laboratoire de Biochimie et Génétique Moléculaire
 Université de La Réunion
 BP 7151, 15 avenue René Cassin
 97715 Saint Denis Messag Cedex 09
 La Réunion
 FRANCE
 Tel : +262 262 938641
 Fax : +262 262 938237
**********************************************************************


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This mail sent through IMP: http://horde.org/imp/