Optimal Pairwise Alignment Tools - University of Missouri - Kansas ...

o
JAligner facilitates user to implement local alignment in user defined programmable
interface, and has a good documentation for the same
Cons
o It doesn’t provide good help documentation, and so the format of input sequences is
unclear.
o It also does not have explicit support for comparing DNA sequences.
Tool 2: EMBOSS Pair wise Alignment Algorithms
EMBOSS at a glance:
EMBOSS is a sequence analysis tool which is used for pair wise sequence analysis to
compare two sequences. It is used to compare either DNA or protein sequences. It makes
use of a program called “NEEDLE”, in order to implement Needleman-Wunsch global
alignment algorithm that finds the optimum alignment of two sequences when
considering the entire length. EMBOSS also makes use of another program called
“WATER”, in order to implement Smith-Waterman local alignment algorithm that
finds the best region of similarity between two sequences. EMBOSS takes two sequences
as input, and allows users to choose gap open and gap extension penalties from a small
range of values, and also makes use of a substitution matrix specified by the user. The
output reflects the amount of similarity between the two sequences, and the possible
alignment, either global or local.
About “NEEDLE” and “WATER”:
“NEEDLE” and “WATER” make use of dynamic programming concepts, to find an
alignment with maximum possible score, where the score of the alignment is equal to the
sum of matches taken from the scoring matrix. “NEEDLE” works best with closely
related sequences. With distant related sequences, it will produce a similarity match
which has little or no biological significance. One drawback of “WATER” is that if two
proteins share more than one common region, for example one has a single copy of a
particular domain and the other has two copies, then it is possible to miss the second and
subsequent alignments. Both “NEEDLE” and “WATER” can be used to compare DNA-
DNA sequences or protein-protein sequences, and memory requirements for both these
programs are proportional to the product of input sequence lengths.
User Manual for EMBOSS:
Below is a brief user manual, which elaborates and describes the usage of emboss for
both global and local alignment. This user manual is written from an end users point of
view considering the fact that he doesn’t have much biological background, but definitely
can familiarize himself with the usage of different online tools.
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