[ensembl-dev] Ensembl Genomes BLAST: empty database comboboxes

Rafael Hernández rafahd87 at gmail.com
Mon Mar 4 13:12:56 GMT 2013

Hi Ensembl devs!

I've got some troubles with Ensembl Genomes BLAST (for fungi, protists, ...)
In the BLAST page the comboboxes for the *dna database* and *protein
database *selection are empty, probably something is misconfigured. Below
the content of the MULTI.ini file:

; Registers blast datasources. Key values are used as labels
; Keys should be registered against methods in species.ini files
CDNA_ALL        = cDNAs
CDNA_ABINITIO   = Ab-initio cDNAs (Genscan/SNAP)
PEP_ALL         = Peptides
PEP_ABINITIO    = Ab-initio Peptides (Genscan/SNAP)
RNA_NC          = Ensembl Non-coding RNA genes
LATESTGP        = Genomic sequence
LATESTGP_MASKED = Genomic sequence (masked)

BLASTN   = [blast dna dna ncbiblastn]  ; alternatives: ncbiblastn,
 ensembl_wublastn, sge_wublastn
BLASTX   = [blast dna peptide ncbiblastx]  ; alternatives: ncbiblastx,
 ensembl_wublastx, sge_wublastx
BLASTP   = [blast peptide peptide ncbiblastp]  ; alternatives: ncbiblastp,
 ensembl_wublastp, sge_wublastp
TBLASTN  = [blast peptide dna ncbitblastn] ; alternatives: ncbitblastn,
ensembl_wutblastn, sge_wutblastn
TBLASTX  = [blast dna dna ncbitblastx] ; alternatives: ncbitblastx,
ensembl_wutblastx, sge_wutblastx
BLAT     = [blat dna dna blat_gfclient]

DATABASE_BLAST = ensembl_blast
HOST = localhost
PORT = 3306
USER = ***********
PASS = ***********

Could you explain a little how should I set these fields?
The Ensembl documentation seems to me a bit confusing when talks about
Blast configuration.

Thank you and best regards,

Rafa Hernández de Diego

SLU-Global Bioinformatics Center
Swedish University for Agricultural Sciences (SLU)
Gerda Nilssons väg 2,
Box 7023, 750 07 Uppsala, Sweden.
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