Question

What is an alignment? How were these used to generate a phylogenetic tree of the mtDNA sequences? Why were alignments important in figuring out if you designed good primers?

What is a mitochondrial haplogroup? How did you determine which one you are most likely to belong to?

Answer 1

An alignment : specifically in bioinformatics DNA, RNA and protein sequences are arranged or alligned on each other such that one can identify regions of similarity. this region of similarity are called matching sequence which are because of functional, structural, or evolutionary relationships between the sequences. As DNA, RNA and protein sequence sizes are very long and alligning each one to each other for similarity checking will take lot of time so for this we use various computer softwares which do the allignment very fast by using various allignmnet algorithms.

for example :

sequence A : ACTGGTACCATG

sequence B : ACTGGTACCCAT

in above DNA sequence allignment the two seqences are totally alligned except the last three nucleotides which may be because of mutation in sequences during evolution.