Review Article

An Overview of Multiple Sequence Alignments and Cloud Computing in Bioinformatics

Table 1

Types of multiple sequence alignment and corresponding algorithms.

Types of MSA alignmentMSA algorithms

Pairwise alignmentNeedleman-Wunsch, k-mer, k-tuple, and Smith-Waterman algorithms.
Progressive alignmentClustal Omega, ClustalW, MAFFT, Kalign, Probalign, MUSCLE, Dialign, ProbCons, and MSAProbs.
Iterative progressive alignmentPRRP, MUSCLE, DIALIGN, SAGA, and T-COFFEE.
Homology search toolsBLAST, PSI-BLAST, and FASTA.
Structure incorporating alignment3D-COFFEE, EXPRESSO, and MICAlign.
Motif alignmentPHI-Blast, GLAM2.
Short-read alignmentBowtie, Maq, and SOAP.