Sequence Align Analysis Command FAQ
Overview
This FAQ contains information related to using the online Sequence Align Analysis Command function. Please direct all corrections and additions to RDP-II General Support (rdp@cme.msu.edu). This FAQ can be found on the Web at http://www.cme.msu.edu/RDP/docs/seq_align_faq.html. Information in this FAQ is primarily based on e-mail received via the RDP-II Support page linked at the bottom of the analysis form.
    Frequently Asked Questions
  1. Q: What does Sequence Align do?
    A: Sequence Align accepts sequence entries and aligns them against the most similar RDP sequence. This method highlights un-ambiguous alignment regions, with ambiguous or uncertain alignment regions displayed in non-highlighted text. These ambiguous regions can be left out of subsequent treeing analyses.

  2. Q:  What base codes are not official IUB base codes?
    A: The IUB (International Union of Biochemistry) created a definition of nucleotide representations. Any non-alphabetic or the letters E, F, I, J, L, O, P, Q, X, and Z are non-IUB base codes.

    The following are the official IUB base codes:

      Unambiguous bases:
      A, C, G &T (or U)
      Either of two bases possible:
      M (A or C)
      R (A or G)
      W (A or T/U)
      S (C or G)
      Y (C or T/U)
      K (G or T/U)
      Any of three bases possible:
      B (C, G or T/U)
      D (A, G or T/U)
      H (A, C or T/U)
      V (A, C or G)
      Any of the four bases possible:
      N (A, C, G or T/U)




 Last updated on 09/03/1999.