Sherbrooke, 18 septembre 1991
I have made a blastp search of two viral sequences (enzyme and structural
protein) against Swiss-prot, PIR and GenBank databases and it worked very well
except for the GenBank search for which I received the message: couldn't open
database file "/blast/db/genbank.head". I also made the same search with
FASTA (against Swiss-prot and GenPept/all) and that also worked.
The question I asked myself looking at those search results is: "why is
the same search algorithm giving the same result for two databases but in
different order... if it is the same search algorithm wouldn't it be more
logical to find the same sequences in the same order?"
Comparing FASTA and Blastp searches: both gave good results for my
searches. They found all the other sequences I knew that were homologous.
Is it possible that Swiss-prot database is more complete than the PIR one?
I cannot tell for GenBank since I had either no result (with Blastp) or I
couldn't interpret the result since it was given in "codes" like ADBCG_20 or
ACNLKTAC_2 (with FASTA). Is there a way I can find out what those codes
correspond to besides from asking the sequences from GenBank? Finally,
how can I succeed a search against GenBank with Blastp? (I used: DATALIB
Merci de votre attention,
Graduate student Sherbrooke Univ.
N.B. Sorry for my bad English...
E-mail: dtang at udesvm.bitnet or dtang at vm1.si.usherb.ca