SignalX parameters

Parameters

• Type of the signal. There are follow types of signal available:
  • General word. No symmetry expected
  • Palidrome. In this case the program selects imperfect palindromes. The profile will not have perfect symmetry
  • Inverted repeat. This type of pattern has two differences from Palindrome.
    1. Variable distance between parts allowed.
    2. The profile will be generated using two parts of the inverted repeat, i.e. every signal will bring two word to the profile - from left and from right part of the repeat
  • Direct repeat. The signal should contain more than one word in one orientation
  • Common repeat. The signal should contain more than one word in arbitrary orientation
• Initial word length. On the first step of the algorithm the program searches for signal of given length. After that it tunes the word length.
• max Mismatch. Max number of mismatches between two words in the profile.
• min distance. Minimum distance between words in inverted/direct/common repeat. This parameter is not used in case of “Word” or “Palindrome” type.
• max distance. Maximum distance between words in inverted/direct/common repeat. This parameter is not used in case of “Word” or “Palindrome” type.

Advanced parameters

• Number of iterations. Usually 3 iteratuins gives good results. But user can change this value.
• Min Z-score. This parameter restricts significance of sites. The sites with Z-score les than given threshold will be ignored.
• Min Average Info. This parameter restricts the average information content of the profile. The profiles with small inforation content will not be shown.
• Portion of additional Rnd Columns To have more presize results we introduce some noice. This parameter defines a portion of additional random columns that will be used for definition the threshold on the information content of the column.
• Portion of additional Rnd Sequences To have more presize results we introduce some noice. This parameter defines a portion of additional random sequences.

Sequence Format

Example of sequence input data