- Forgetting the wild card in the database filename
The wild card is important. First because it masks the
time-stamp or version number. Second, because it allows the database to be updated without interrupting ongoing
searches. Even if you don't want to use a time-stamp or version number, you must still include a wild card.
- Putting the wild card in the filename extension
The wild card is there to mask the time-stamp or
version number, not the extension. The filename should be like MSDB_*.fasta or MSDB*.fasta. If you specify the
filename as MSDB.*, then Mascot won't be able to distinguish the Fasta file from the Reference file, with
interesting results.
- Using spaces or special characters in the database path
Spaces in paths may be legal in Windows, but they
shouldn't be. Besides a wild card in the filename, only alphanumerics and the
following characters are permitted in paths: /:_.-$%&()[]
- Using back slashes in the database path
Even if you are running Mascot on a Windows platform, all paths must use forward slashes.
- Out of date taxonomy files
The taxonomy files need to be of a similar date to the Fasta file. These
files are used to create a taxonomy index at the time the Fasta file is compressed, so its no use updating
the files afterwards.
- Creating a sequence database with inconsistent title syntax
If you merge two or more Fasta files into a single file, you need to ensure that a unique identifier (accession)
can be parsed from all entries with a single parse rule. It may be necessary to use a few lines of Perl to reformat
the title lines, rather than just copying or cat'ing the files together.