Probe design, probe matching, and searching the nearest relatives require a lot of database searching. Simply scanning the whole database for a specific target takes several tens of seconds. Probe design and searching for nearest relatives start thousands of search operations. Waiting several weeks to get a result from the computer makes every user hate the program, so better algorithms have to be developed.
The basic ARB SEARCH ALGORITHM:
When any (calling) program wants to scan a database, it does not do the job itself but calls a special SEARCH_PATTERNS_IN_A_BIG_DATABASE_PROGRAM.
We named this program PT_SERVER ('Prefix tree server' or synonymously 'Positional tree server'). The PT_SERVER searches for patterns in special database files and sends all matches back to the calling program.
Different databases have different PT_SERVERs. You must choose a PT_SERVER to match the database you wish to search. The file $ARBHOME/lib/arb_tcp.dat defines all possible choices.
If there is no PT_SERVER running, one is automatically started. A PT_SERVER does not scan the database of the calling program, but the database in $ARBHOME/lib/pts/*.arb.
If you have just entered a new sequence this sequence will not be found by the the nearest-relative search.
This is normally very useful, as you only want to use old sequences as a reference in the aligning process.
For generating probes it isn't useful, because new sequences have to be added to the PT_SERVER before designing or matching probes. Remember: By adding 1 new sequence to the database, any previously validated probe may become invalid.
Re-build your PT-server frequently and re-evaluate any probes you've made before.
Creating a new PT_SERVER template:
Edit the file $ARBHOME/lib/arb_tcp.dat using <ARB_NTREE/Probes/PT_SERVER Admin/CREATE TEMPLATE>
Note: Make a copy of your changes because a new ARB installation may reinstall and overwrite your changed $ARBHOME/lib/arb_tcp.dat.
Create a database for an existing template:
Start ARB with the database you want to send to the PT_SERVER.
Open the PT_SERVER ADMIN Window <ARB_NTREE/Probes/PT_SERVER Admin>.
Select a template
Press <BUILD SERVER>: ARB will save the DB into $ARBHOME/lib/pts/name.arb
ARB generates an index file $ARBHOME/lib/pts/name.arb.pt
If any '*.arb' file in $ARBHOME/lib/pts is newer than the corresponding '*.arb.pt' ( == prefix tree) file the '*.arb.pt' file will be updated as soon as the PT_SERVER is started.
Updating a server:
see 'Create a database for an existing template'.