Blast analysis - help in interpretation

krishnan at BORCIM.WUSTL.EDU krishnan at BORCIM.WUSTL.EDU
Tue Jul 26 18:32:18 EST 1994


Hello everybody!
Could somebody help me in the interpretation of the following Blast
analysis results?  I obtained 266 bp of human genomic sequence and did both
Blastx and Blastn analyses and the results were as follows (abbreviated
for sake of discussion):

Blastx results:
Sequences producing high-scoring High score Smallest Poisson Probability
Large T antigen TVV              408        1.6e-51
large T [Rhesus macaque polyoma] 408        1.6e-51
Large T [Papovavirus]            357        2.7e-44
Tantigen[Bovine papilloma virus] 144        3.9e-14
Tantigen[Mouse polyoma virus]     97        1.2e-12

The identity at the amino acid sequence level were: 77-91% in the
high scoring pairs and the length of the aa sequences compared were
72-94 in continous stretches.

Blastn results:
Sequences producing high scoring High score Smallest Poisson probability
Synthetic plasmid pDSP1          1232       3.9e-95
vector pBLCCAT6 encoding CAT     1231       4.7e-95
etc, etc most of which is CAT plasmids and the nt homology is 98-100% over
the 266 nt stretch.

My questions are:
1. What do I infer from the following?  (is the DNA I sequenced portion of
CAT gene?)
2. The Blastx and Blastn analyses seem to be inconsistent, i.e., why did 
the CAT homology not show up in the Blastx analysis (I am searching against 
a non-redundant database)?
3. When sequencing anonymous human DNA, which Blast analysis is best to use
.

	I found this not only with the above clone, but with also another 
clone, which by Blastx analysis is homologous to a protein sequence in the 
database (and consistent with the cytologic mapping of this gene in this 
portion of the human genome), but has no homology (in Blast analysis and by 
sequence-sequence comparison).  Any pointers and help in interpreting these 
are highly appreciated.
Raja
p.s.: I am not a subscriber to the network, therefore please email your 
replies to krishnan at borcim.wustl.edu



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