CSE 427, Wi '21: Assignment #1 examples

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Here are two quick examples of Smith-Waterman scoring and alignments, using Blosum62 and linear gap costs with a score of -4 per position, as requested in the assignment. Note:

that the output format here isn't quite what the assignment sheet suggested, and
that you only need to print ONE optimal alignment, not all.

Otherwise this should give you some simple examples against which to check your program. Ask if you persistently get different answers; my solution may be faulty. The excel spreadsheet(s) linked from the home page (or here) may also be helpful.

KEVLAR vs KNIEVIL

  |    K  N  I  E  V   I   L
--+-------------------------
  | 0  0  0  0  0  0   0   0
K | 0  5  1  0  1  0   0   0 
E | 0  1  5  1  5  1   0   0 
V | 0  0  1  8  4  9   5   1 
L | 0  0  0  4  5  5  11   9 
A | 0  0  0  0  3  5   7  10 
R | 0  2  0  0  0  1   3   6 

--KEVLAR
   |||
KNIEVIL-
  Score=11

Formatted as requested in the assignment, this might look like:

seqid001: 2 EVL
            EV+
seqid002: 4 EVI

MELLSLCSWFAAATTYDADFYDDP vs MSNWTATSSDSTS

  |     M   E   L   L   S   L   C   S   W   F   A   A   A   T   T   Y   D   A   D   F   Y   D   D   P
--+--------------------------------------------------------------------------------------------------
  | 0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
M | 0   5   1   2   2   0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
S | 0   1   5   1   0   6   2   1   4   0   0   1   1   1   1   1   0   0   1   0   0   0   0   0   0
N | 0   0   1   2   0   2   3   0   2   0   0   0   0   0   1   1   0   1   0   2   0   0   1   1   0
W | 0   0   0   0   0   0   0   1   0  13   9   5   1   0   0   0   3   0   0   0   3   2   0   0   0
T | 0   0   0   0   0   1   0   0   2   9  11   9   5   1   5   5   1   2   0   0   0   1   1   0   0
A | 0   0   0   0   0   1   0   0   1   5   7  15  13   9   5   5   3   0   6   2   0   0   0   0   0
T | 0   0   0   0   0   1   0   0   1   1   3  11  15  13  14  10   6   2   2   5   1   0   0   0   0
S | 0   0   0   0   0   4   0   0   4   0   0   7  12  16  14  15  11   7   3   2   3   0   0   0   0
S | 0   0   0   0   0   4   2   0   4   1   0   3   8  13  17  15  13  11   8   4   0   1   0   0   0
D | 0   0   2   0   0   0   0   0   0   0   0   0   4   9  13  16  12  19  15  14  10   6   7   6   2
S | 0   0   0   0   0   4   0   0   4   0   0   1   1   5  10  14  14  15  20  16  12   8   6   7   5
T | 0   0   0   0   0   1   3   0   1   2   0   0   1   1  10  15  12  13  16  19  15  11   7   5   6
S | 0   0   0   0   0   4   0   2   4   0   0   1   1   2   6  11  13  12  14  16  17  13  11   7   4

MELLSLCSWFAAATTYDADFYDDP
     |||||||||||||
-----MSNW-TA-TSSDSTS----
  Score=20

MELLSLCSWFAAATTYDADFYDDP
     |||||||||||||
-----MSNW-T-ATSSDSTS----
  Score=20

MELLSLCSWFAAATTYDADFYDDP
     |||||||||||||
-----MSNW--TATSSDSTS----
  Score=20

Formatted as requested in the assignment, the 3rd of these might look like:

seqid003: 6 LCSWFAAATTYDA
            + +W   AT+ D+
seqid004: 1 MSNW--TATSSDS


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