[Genome] gfServer misses result

[Nobuyuki Kawagashira]

Dear all,

I already performed standalone BLAT to search for 474 known pre-miRNA
sequences of median 90 bp on the whole hg18 human genome, finding all
their loci. But I set gfServer using a single 2bit database created by
faToTwoBit from multiple chromosomal FASTA files and used gfClient with
the same parameters. But gfClient provided me only two known alignment
results (out of 474).
gfServer parameters are follows: -tileSize=7 -stepSize=7.
Changing gfClient parameters, -minScore=0 and -minIdentity=0, did not
improve the result with only two.
I also set gfServer with multiple .2bit and .nib files as database. But
gfClient resulted in giving the same two records.
I used blat suite 3.3 executables for solaris. Platform is Sun Sparc
Solaris 8. Do anybody know any solutions to it? Thank you in advance.

Nobuyuki Kawagashira