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Last update on 04. Dec 2013 .
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Nearest relative search

OCCURRENCE

ARB_NT/Search/More search/Search Next Relatives of SELECTED Species in PT Server ARB_NT/Search/More search/Search Next Relatives of LISTED Species in PT Server ARB_NT/ARB_EDIT/EDIT/Integrated Aligners

 

ALGORITHM

Splits the sequence(s) into short oligos of a given size. These oligos are 'Probe Matched' against the PT_SERVER database. The more hits within the sequence of another species, the more related the other species is.

 

PARAMETERS

PT-Server

Select the PT-Server to search

Oligo length

Length of oligos used to perform probe match against the PT server. Default is 12.

Mismatches

  • Number of mismatches allowed per oligo. Default is 0.
  • Be careful: The search may get incredible slow, when rising the number of mismatches.

Search mode

  • Complete:        Match all possible oligos
    Quick:           Only match oligos starting with 'A'
  • The 'Quick mode' works well for many sequence types and is approx. 4 times faster than the 'Complete mode'. For some sequence types it completely fails, e.g. if there are repetitive areas containing many 'AAAAA'

Match score:

  • absolute:        returns the absolute number of hits
    relative:        returns the number of hits relative to maximum possible hits
  • The score depends on several other parameters like number of allowed mismatches, search mode, oligo length and complement settings.
  • The maximum absolute score is

    (length of relatives sequence) minus (oligo length)

  • Practically this score is rarely reached, because several possible oligos are skipped, namely
    • all oligos starting with 2 identical nucleotides
    • all oligos containing IUPAC codes (or N's)

  • If mismatches are used, each oligo may hit at several positions. Thus the maximum relative score may exceed 100% (and the maximum absolute score may exceed its theoretical maximum).
  • If you use 'Quick mode' the mean relative score will be approx. 25% (assuming that 25% of the possible oligos start with an 'A').
  • That means.. only if you use
    • 0 mismatches,
    • 'Complete mode' and
    • your sequences contain no IUPACs and no repetitions,

  • you will get a score of 100% (or sequenceLength-oligoLength) for the selected species itself and its duplicates.

Complement:

  • forward:             Match only forward oligos
    reverse:             Match only reverse oligos
    complement:          Match only complement oligos
    reverse-complement:  Match only reverse-complement oligos
    and all combinations of these.
  • The combinations may affect the score as well!
  • Note: Not available for EDIT4 aligner.

 

NOTES

None

 

EXAMPLES

None

 

WARNINGS

None