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URGENT help FASTA on GCG

Rodrigo Lopez rodrigol at biomaster.uio.no
Sat Apr 9 15:36:28 EST 1994


In article <2o18ks$b0v at mserv1.dl.ac.uk>, "A. Kalogeropoulos" <angelos at igmors.u-psud.fr> writes:
|> 
|> >
|> > *** Error: Cannot open file FUN:SCCHROMI
|> >
|> >
|> >
|> > What is the cause of this error ?
|> >
|> 
|> You have to specify EM_FUN:SCCHROMI (and not FUN:SCCHROMI)
|> 

Check the following first:

1 .  cd $GCGSYSTEMROOT/gcgcore/data/rundata

     check that the file dbnames.map has the following entries
     for embl:

inv             em_in           in              ! embl invertebrate
phg             em_ph           ph              ! embl bacteriophage
fun             em_fun          pl              ! embl fungi
org             em_or           or              ! embl organelle
mam             em_om           om              ! embl other mammal
vrt             em_ov           ov              ! embl other vertebrate
pln             em_pl           pl              ! embl plant
pri             em_pr           pr              ! embl primate
pro             em_ba           ba              ! embl prokaryote
rod             em_ro           ro              ! embl rodent
syn             em_sy           sy              ! embl synthetic
unc             em_un           un              ! embl unannotated
vrl             em_vi           vi              ! embl virus
bb              em_bb                           ! embl backbone sequences
patent          em_pat          pat             ! embl patent sequences
est             em_est          est             ! embl est sequences

2. check that embl.farm corresponds with this file.


3. If the above is a hassle make sure to check the header files
   on the gcgdata/gcgembl directory. My bet is that there is something
   unspecified here, like embldir:fu. If this is true it should read
   embldir:em_fun. The long name and short names can be FUN and FU if
   you like, but fasta reads the full name for retrieval during 
   the alignment step.




Hope this helps.



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