source: trunk/HELP_SOURCE/source/optimize.hlp

Last change on this file was 19532, checked in by westram, 5 weeks ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 1.4 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#SUB     subtopic.hlp
6
7
8TITLE           Optimize database compression
9
10OCCURRENCE      ARB_NT
11
12DESCRIPTION     Sequence data normally need's a lot of memory. To be able to
13                handle thousands of sequences we implemented an online
14                compression. All data is compressed most of the time and only
15                uncompressed on demand. As a user you only find smaller database
16                files, that's all.
17                Without understanding the data, the program can compress data only
18                by a limited factor. With the help of a tree aligned sequences
19                can be compressed much better by storing only the differences
20                to a consensus sequence.
21                Once a sequence is compressed using a tree, it will keep
22                the good compression method until it is changed. Then only the
23                older method is used.
24                As long as you change only a few (up to 100) sequences, the
25                database won't grow very much.
26
27                To compress the entire database, the program needs a tree,
28                which should cover most of the sequences. The larger and better
29                the tree, the better the compression.
30
31EXAMPLE         10000 aligned 16s sequences need 50 mega-bytes of memory.
32                Without your help ARB will reduce them to 10 mega-bytes,
33                and given a tree not more than 2 mega-bytes will be needed.
34
35
36NOTES           Any major database update, especially inserting or deleting
37                gaps in an alignment, should be followed by a new optimization
38                step.
39
40BUGS            No bugs known
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