DNA-Sequence-Alignment

Perl Implementation of a three different techniques for DNA or Protein sequence alignment to calculate similarity between 2 or more sequences by searching for a series of individual characters that are in the same order in the sequences.

In Bioinformatics there are a technique called sequence alignment It is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.

Example:

sequence pair 1:

TGGTAGATTCCCACGAGATCTACCGAGTATGAGTAGGGGGACGTTCGCTCGG GCCTCTAACACACTGCACGAGATCAACCGAGATATGAGTAATACAGCGGTACGGG

sequence pair 2:

CTGTCGCTGCACG TGCCGTG

sequence pair 3:

CAGCACTTGGATTCTCGG CAGCGTGG

Results and conclusion:

\	Global Alignment	Semi-Global Alignment	Local Alignment
sequence pair 1	77	97	106
sequence pair 2	-4	21	21
sequence pair 3	-10	21	21

Alignment G1:

TGG-T--AGATTC-C--CACGAGATCTACCGAG-TATGAGTAGGGGGAC-GTTCGCT-CGG-

-GCCTCTA-ACACACTGCACGAGATCAACCGAGATATGAGTAAT---ACAG--CGGTACGGG

Alignment G2:

CTGTCGCTGCACG

-TGCCG-TG----

Alignment G3:

CAGCACTTGGATTCTCGG

CAGC----G--T----GG

Alignment S1:

---TGGTAGATTC-C--CACGAGATCTACCGAG-TATGAGTAGGGGGAC-GTTCGCT-CGG-

GCCTC-TA-ACACACTGCACGAGATCAACCGAGATATGAGTAAT---ACAG--CGGTACGGG

Alignment S2:

CTGTCGCTGGCAC

-TGCCG-TG----

Alignment S3:

CAGCACTTGGGGCTCTTA

CAGCG-T-GG--------

Alignment L1:

CACGAGATCTACCGAG-TATGAGTA

CACGAGATCAACCGAGATATGAGTA

Alignment L2:

TGTCGCTG

TGCCG-TG

Alignment L3:

CAGCACTTGG

CAGCG-T-GG

Notes on these results:

• Semi Global Alignment is always better than Global Alignment.

• Local Alignment is always better than the Global Alignment and maybe equal to the scores in the semi global Alignment.

• The semi-global alignment algorithm was able to detect better than the global alignment algorithm.

• The local alignment algorithm was able to detect region(s) of similarity that were overlooked by the global alignment.