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Fasta says "No sequences to compare to query sequence!"

You may have typed in the database name incorrectly. For example, the following responses would be incorrect:
  Search for query in what sequence(s) (* GenEMBL:* *) ?  genbank
  Search for query in what sequence(s) (* GenEMBL:* *) ?  embl 
  Search for query in what sequence(s) (* GenEMBL:* *) ?  genbank:
  Search for query in what sequence(s) (* GenEMBL:* *) ?  all
and Fasta will say:
   *** No sequences to compare to query sequence! *** 
You need the ":*" after the database name in order for Fasta to search it correctly. Here are some correct responses:
  Search for query in what sequence(s) (* GenEMBL:* *) ? 
(i.e. if you simply hit a carriage return (Enter), Fasta will search the default database. For nucleic acid query sequences this is GenEMBL, and for protein query sequences the default is Swissprot).
  Search for query in what sequence(s) (* GenEMBL:* *) ?  genbank:*
(This is the correct syntax for the database name).
  Search for query in what sequence(s) (* GenEMBL:* *) ? *
Here the syntax is correct, but the '*' tells Fasta to search through all the sequence files in your own current directory, and not through any database. If this is what you want, you're ok.

Another possibility is that you were trying to search EMBL? On the helix systems, we primarily maintain Genbank, and only keep those entries from EMBL that do not appear in EMBL. Since EMBL and Genbank largely overlap, many of the EMBL databases (such as em_pat, em_gss) are empty or have very few sequences. Try the equivalent Genbank databases instead (e.g. gb_pat or gb_gss).