08-16-2017, 09:06 PM
[attachment=15163]
Sequence 1:
>gi 150393488 ref YP_001316163.1 globin [Staphylococcus aureus subsp. aureus JH1]
MTTPYDIIGKEALYDMIDYFYTLVEKDERLNHLFPGDFAETSRKQKQFLTQFLGGPNIYTEEHGHPMLRKRHMDFTITEFERDAWLENMQTAINRAAFPQGVGDYLFERLRLTANHMVNS
Sequence 2:
>gi 57637203 gb AAW53991.1 protozoan/cyanobacterial globin family protein [Staphylococcus epidermidis RP62A]
MSIRQITFKCKNSCYIRYILMEHGDIMSKTPYELIGQKALYQMIDHFYQLVEKDSRINHLFPGDFKETSRKQKQFLTQFLGGPDLYTQEHGHPMLKRRHMEFTISEYERDAWLENMHTAIQHAELPAGVGDYLFERLRLTAHHMVNS
Theory:
The method used to analyze the similarities and differences at the level of individual bases or amino acids with the aim of inferring structural, functional and evolutionary relationships among the sequences are called sequence alignment.
A sequence alignment is a scheme of writing one sequence above of another where the residues in one position are deemed to have a common evolutionary origin. If the same letter occurs in both sequences then this position has been conserved in evolution. If the letters differ it is assumed that the two derive from an ancestral letter (which could be one of the two or neither). Homologous sequences may have different lengths, because of insertions or deletions in either sequence.
Thus, a letter or a stretch of letters may be paired up with dashes in the other sequence to signify such insertions or deletions. Since an insertion in one sequence can always be seen as a deletion in the other one frequently uses the term "indel".
An alignment assumes that the two proteins or DNA sequences are basically similar to one another over the entire length. The alignment attempts to match them to each other from end to end, even though parts of the alignment are not very convincing.
Global alignment is performed by Needleman-Wunsch algorithm.
Procedure:
Respective protein sequences of Staphylococcus aureus (YP_001316163.1) and Staphylococcus epidermidis (AAW5399.1) in Fasta format were retrieved from NCBI (ncbi.nlm.nih.gov).
Log in to http://ebi.ac.uk/Tools/emboss/align/
Paste the respective sequences in the given input boxes.
Keep the method in Needle (global) tool and remaining option buttons in default.
Click run.
Results were displayed as soon as the given job completed.