Python 2.6.5 (r265:79063, Apr 16 2010, 13:09:56) 
[GCC 4.4.3] on linux2
Type "copyright", "credits" or "license()" for more information.

    ****************************************************************
    Personal firewall software may warn about the connection IDLE
    makes to its subprocess using this computer's internal loopback
    interface.  This connection is not visible on any external
    interface and no data is sent to or received from the Internet.
    ****************************************************************
    
IDLE 2.6.5      
>>> import dp
>>> help(dp)
Help on module dp:

NAME
    dp - Dynamic programming examples

FILE
    /home/karmic/Projects/Courses/BmsMinicourse/examples2/dp.py

FUNCTIONS
    nw(seq1, seq2, s, e=-1, debug=False)
        Return an optimal global alignment of seq1 and seq2
        given scoring matrix s (a dictionary of dictionaries),
        and gap extension penalty e.
        All scores are assumed to be integers.
    
    nw_dump(seq1, seq2, m, p)
        Print a diagnostic dump of the results of nw_fill.
    
    nw_fill(seq1, seq2, s, e)
        Return the score and pointer matrices from the dynamic
        programming step of Needleman-Wunsch.
    
    nw_traceback(seq1, seq2, p)
        Return the alignment corresponding to the "middle-road" traceback
        of the given pointer matrix.

DATA
    ident = {'A': {'A': 1, 'C': -1, 'G': -1, 'T': -1}, 'C': {'A': -1, 'C':...


>>> s1 = "AGCGGTA"
>>> s2 = "GAGCGGA"
>>> dp.nw(s1,s2,dp.ident)
('-AGCGGTA', 'GAGCGG-A')
>>> aligned = dp.nw(s1,s2,dp.ident)
>>> print "\n".join(aligned)
-AGCGGTA
GAGCGG-A
>>> aligned = dp.nw(s1,s2,dp.ident, debug = True)
         G    A    G    C    G    G    A
    0   -1   -2   -3   -4   -5   -6   -7     
   -1   -1    0   -1   -2   -3   -4   -5    A
   -2    0   -1    1    0   -1   -2   -3    G
   -3   -1   -1    0    2    1    0   -1    C
   -4   -2   -2    0    1    3    2    1    G
   -5   -3   -3   -1    0    2    4    3    G
   -6   -4   -4   -2   -1    1    3    3    T
   -7   -5   -3   -3   -2    0    2    4    A

[None, [(0, 0)], [(0, 1)], [(0, 2)], [(0, 3)], [(0, 4)], [(0, 5)], [(0, 6)]]
[[(0, 0)], [(0, 0)], [(0, 1)], [(1, 2)], [(1, 3)], [(1, 4)], [(1, 5)], [(0, 6), (1, 6)]]
[[(1, 0)], [(1, 0)], [(2, 1), (1, 2)], [(1, 2)], [(2, 3)], [(1, 4), (2, 4)], [(1, 5), (2, 5)], [(2, 6)]]
[[(2, 0)], [(2, 1)], [(2, 1)], [(2, 3)], [(2, 3)], [(3, 4)], [(3, 5)], [(3, 6)]]
[[(3, 0)], [(3, 0), (3, 1)], [(3, 1), (3, 2)], [(3, 2)], [(3, 4)], [(3, 4)], [(3, 5), (4, 5)], [(4, 6)]]
[[(4, 0)], [(4, 0), (4, 1)], [(4, 1), (4, 2)], [(4, 2), (4, 3)], [(4, 4)], [(4, 4), (4, 5)], [(4, 5)], [(5, 6)]]
[[(5, 0)], [(5, 1)], [(5, 1), (5, 2)], [(5, 3)], [(5, 4)], [(5, 5)], [(5, 6)], [(5, 6)]]
[[(6, 0)], [(6, 1)], [(6, 1)], [(6, 3)], [(6, 4)], [(6, 5)], [(6, 6)], [(6, 6)]]
>>>