relax SVN archive

Fix for the Needleman-Wunsch sequence alignment algorithm.

The start of the sequences are no longer truncated when starting gaps are encountered.

Created a unit test for demonstrating a failure in the Needleman-Wunsch sequence alignment algorithm.

The test is Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4b from the
_lib._sequence_alignment.test_needleman_wunsch module. The problem is that the start of the
alignment is truncated if any gaps are present.

Created the Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4 unit test.

This is in the unit test module _lib._sequence_alignment.test_needleman_wunsch. This tests the
Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.

Modified the Test_needleman_wunsch.test_needleman_wunsch_align_DNA unit test to pass.

This is from the unit test module _lib._sequence_alignment.test_needleman_wunsch. The DNA sequences
were simplified so that the behaviour can be better predicted.

Added the PAM 250 amino acid substitution matrix.

This was taken from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM250 and added to
lib.sequence_alignment.substitution_matrices.PAM250.

Added the header from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62.

This is to document the BLOSUM62 substitution matrix.

Added the NUC 4.4 nucleotide substitution matrix from ftp://ftp.ncbi.nih.gov/blast/matrices/.

Uracil was added to the table as a copy to T.

Added sanity checks to the Needleman-Wunsch sequence alignment algorithm.

The residues of both sequences are now checked in needleman_wunsch_align() to make sure that they
are present in the substitution matrix.

Added a DNA similarity matrix to lib.sequence_alignment.substitution_matrices.

Modified the Needleman-Wunsch sequence alignment algorithm.

The previous attempt was buggy. The algorithm has been modified to match the logic of the GPL
licenced EMBOSS software (http://emboss.sourceforge.net/) to allow for gap opening and extension
penalties, as well as end penalties. No code was copied, rather the algorithm for creating the
scoring and penalty matrices, as well as the traceback matrix.