Extract upstream sequences

• Retrieval of more than the direct upstream sequence of a gene is possible. This is sometimes necessary if the gene belongs to an operon.
  • gap
    Defines the operon as a chain of genes where tandem genes must have smaller gaps between them than this value.
  • min gap
    If a gap between genes of an operon is smaller than this value it is not included as one of the upstream sequences, otherwise it is.
  • Max operon seq
    The operon upstream sequence is the upstream sequence of the whole operon (the last upstream sequence in the chain). One can set a maximum extraction length for it.
  • Min operon seq
    The operon upstream sequence is not printed if it is smaller than this value.
• The upstream of a gene is defined as the upstream sequence of the gene and the upstream sequences of all the other genes before it in the same operon. These are the extraction modes.
  • Gene upstream sequences only
    Only the immediate upstream sequence (the first in the chain) is retrieved.
  • All upstream sequences of gene in operon
    The whole chain of upstream sequences is retrieved. The starting sequence for the operon search is indicated in parenthese, eg, (Rv0350/1), (Rv0350/2), ...
  • Operon upstream sequence only
    Only the last gene in the chain is retrieved. The starting gene for the operon search indicated in parentheses, eg, (Rv0350/o).
• Note that multiple sequences are suppressed. If several genes share an operon, it might be that in the operon sequence retrieval mode one upstream sequence is retrieved only for all of them.

Gibbs and Alignace

• width
  The width of the expected motif.
• expected
  The approximate number of motifs expected. Note that one sequence may contain several occurences of the same motif or none at all.
• seed
  These are probabilistic programs using the date to start the random number generator; to repeat a result the seed needs to be noted after a run and entered explicitely next time.

Palindrome

• width
  The width of the expected motif.
• p-value palindrome
  The more mirror sites there are in a palindrome the lower (better) the p-value. For very small values only true palindromes are accepted at all.
• p-value iteration
  A motif initially only consists of one palindrome. In an iteratitive search it is expanded by further palindromes matching the growing motif. The lower the iteration p-value the harder it is to find matching palindromes, and consequently the motifs comprise fewer sequences.