[ssml] error from BLASTCLUST

Manoj Tyagi Manoj.TYAGI at univ-reunion.fr
Thu Sep 2 09:18:56 EDT 2004


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 

Could you help me out, what to do in this case. & why it is giving error? 

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
 Tel : +262 262 938641
 Fax : +262 262 938237

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