Fine tuning the installation:

It is probably a good idea to set up subsections of the database so that end users can search just the regions they wish to search. This section applies to all access methods that use EMBLCD style indexes and probably to others as well.

Files can be included with the declaration

file:

or excluded with the declaration

exclude:

. It is a good idea to put the wild card directory specifier (

*/

)in front of the filename to ensure that any path that may be included in

division.lkp

will be matched. Please note especially the notes for GCG formatted databases indexed with dbigcg.

In order to just take the EST files in our EMBL database try the following:

DB emblest [
   type: N
   method: emblcd
   format: embl
   dir: \$emboss_db_dir/embl
   file: "est*.dat"
   release: "63.0"
   comment: "EMBL release 63.0"
]

Files can also be given as a space separated list enclosed in quotes. For example to set up a database of all mamallian sequences (except genomes) try the following:

DB emblallmam [
   type: N
   method: emblcd
   format: embl
   dir: \$emboss_db_dir/embl
   file: "rod*.dat hum*.dat mam*.dat"
   release: "63.0"
   comment: "EMBL release 63.0"
]

As you can see from these two examples, the

file:

tag takes a space delimited list of filenames enclosed in quotes that can contain normal wildcard (

?*

) characters.

It can be quite tedious to set up a long list of sequences to search. In many cases you can use the

exclude:

tag to make things easier.

DB emblnoest [
   type: N
   method: emblcd
   format: embl
   dir: \$emboss_db_dir/embl
   file: "*.dat"
   exclude: "est*.dat"
   release: "63.0"
   comment: "EMBL release 63.0"
]

This configures the

emblnoest

database to contain all of EMBL except the EST's.