FASTA moans and questions

Reinhard Doelz doelz at comp.bioz.unibas.ch
Mon May 18 12:51:46 EST 1992


In article <9205181427.AA02797 at calshp.cals.wisc.edu>, triplett at CALSHP.CALS.WISC.EDU writes:
|> 	I am also unable to use fasta to search through a specific 
|> subset of sequences, specifically bacterial sequences.  Has GCG

Sounds a bit weired, but surely is a configuration problem. 
Did you use Bill Pearsons's or the GCG version? 
Did you install the databases directly from GCG tape, or did you format 
it yourself?  I recompile EMBL and several other databases daily on 
both VMS and UNIX GCG versions without problems. Let me assume that 
you are on a VMS system and talk about the GCG V7.0x version of FASTA. 
Then, do a 

$ GCG 
$ show logical *BA*

you should get a screenful answers, amongst them something like
"GB_BA" = "GENBANKDIR:GB_BA"

Now, do a 

$  dir/size gb_ba
and you should see several files, including the sizes. The interesting 
part is the header file  .  look at it with 

$type genbankdir:gb_ba.header

You will see a NAME: , a LN: and a SN: field. If all of the names defined 
there are defined under VMS, (and they should), check the protection of 
the files. Can you read these? Next, do 

$ names gb_ba:*

If you don't get it, you are in trouble. Try to see whether 'someone'
has modified FASTA (as I did, for example),  with 

$ sh sym FASTA 
That should point to $GENUTIL:FASTA. If it still doesn't work, try 
to see whether your sequence is recognized as peptide (???)... 


If you did all the commands above and still didn't come accross the trouble, 
repost the replies and we can work on it. 
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