[BiO BB] Unigene FormatDB error on Mac OS X

Tristan Fiedler tfiedler at rsmas.miami.edu
Thu Sep 4 17:12:39 EDT 2003

Thanks all for the hardware tips!

I am currently setting up a blast run of marine sequences against Ciona
intestinalis from Unigene.  A couple of bugs, which  maybe someone has
overcome :

1.  In the file which I downloaded 'File: Cin.seq.uniq.Z', the various
entries in this FASTA format file have headers such as :

>gnl|UG|Cin#S6667694 Ciona intestinalis cDNA, clone:cits020m24, full
insert sequence. /gb=AK117037 /gi=23589844 /ug=Cin.3 /len=12

How can I get a more descriptive/functional definition of the various
unigene clusters?

2.  I used the 'formatdb -i Cin.seq.uniq -p F -o T -n unigene_ciona'
command.  Is this correct?  In the formatdb logfile, how can the following
errors be corrected (if necessary) :

/Users/tfiedler/Desktop/blast.darwin/UNIGENE_DOWNLOAD% more formatdb.log

========================[ Sep 4, 2003  4:53 PM ]========================
Version 2.2.6 [Apr-09-2003]
Started database file "Cin.seq.uniq"
NOTE: CoreLib [002.003]
FileOpen("/Users/tfiedler/Library/Preferences/formatdb.cnf","r") failed
NOTE: CoreLib [002.003]
NOTE: CoreLib [002.003] FileOpen(".formatdbrc","r") failed
NOTE: CoreLib [002.003] FileOpen("/Users/tfiedler/.formatdbrc","r") failed
NOTE: [000.000] No number of link bits used found in config  file. Ignoring
NOTE: [000.000] No number of membership bits used found in config file.
Formatted 13699 sequences in volume 0

Thank you all very much for the assistance!!!


Tristan Fiedler

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