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Old 11-29-2011, 08:25 PM   #1
Daniel Fernandez
Location: Lima. Perú

Join Date: Nov 2011
Posts: 31
Default TGICL fasta vs refdb


I'm using tgicl for clustering EST,
I don't want to it perform all-vs-all, I want to it perform my EST against TIGR gene index <refDb>, how I can do that?.

I use

tgicl -F myEST.fasta -c 1 -p 95 -l 50 -v 20 -O '-p 95 -o 50 -y 20'
I think that I have to use the -d parmeter. In the help says

-d   do not perform all-vs-all search, but search <fasta_db> against
      <refDb> instead; exit after the pairwise hits are generated
May be it is similar to a local blast, download a database or create a database but in a local blast I have to call to the database [blastn -query input -out output -db database] with an alias (for example database.nal - for nucleotide) but with tgicl I don't know how I call the database.

Help please


Last edited by Daniel Fernandez; 11-30-2011 at 08:31 PM.
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est, tgicl, tigr

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