source: tags/arb-6.0.5/HELP_SOURCE/oldhelp/optimize.hlp

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UP      arb.hlp
UP      glossary.hlp

#SUB    subtopic.hlp


TITLE           Optimize Database

OCCURRENCE      ARB_NT

DESCRIPTION     Sequence data normally need's a lot of memory. To be able to 
                handle thousands of sequences we implemented an online
                compression. All data is compressed most of the time and only
                uncompressed on demand. As a user you only find smaller database
                files, that's all.
                Without understanding the data, the program can compress data only
                by a limited factor. With the help of a tree aligned sequences
                can be compressed much better by storing only the differences
                to a consensus sequence.
                Once a sequence is compressed using a tree, it will keep
                the good compression method until it is changed. Then only the
                older method is used.
                As long as you change only a few (up to 100) sequences, the
                database won't grow very much.

                To compress the entire database, the program needs a tree,
                which should cover most of the sequences. The larger and better
                the tree, the better the compression.

EXAMPLE         10000 aligned 16s sequences need 50 mega-bytes of memory.
                Without your help ARB will reduce them to 10 mega-bytes,
                and given a tree not more than 2 mega-bytes will be needed.


NOTES           Any major database update, especially inserting or deleting
                gaps in an alignment, should be followed by a new optimization
                step.

BUGS            No bugs known