Server for multiple alignment of RNA sequences

General Algorithm

  1. Given word length and max number of mismatches
    1. Use MEME algorithm for define conserved blocks

    2. Apply the Dynamic programming algorithm to create chain of the blocks
    3. Refine the chain using combined profile for chain of blocks. The variation of distances between blocks produces gap penalty.

  2. Reduce word length and number of mismatches and repeat the procedure for spacer between the blocks. Repeat the procedure until word size >3

  3. Find potential helices on the sequences with given perameters (loop soze and energy)
  4. Create helix profile and apply MEME-like iterative procedure to find sets of helices that consistent lokated reative to conserved blocks


Andrey Mironov

Department of Department of Bioengineering and Bioinformatics, MSU, Moscow, Russia

Mail to Andrey Mironov