Multiple Sequence Alignment Protein engineering

1 multiple sequence alignment

1.1 clustal omega
1.2 mafft
1.3 k-align
1.4 multiple sequence comparison log expectation (muscle)
1.5 t-coffee

multiple sequence alignment

without structural information protein, sequence analysis useful in elucidating information protein. these techniques involve alignment of target protein sequences other related protein sequences. alignment can show amino acids conserved between species , important function of protein. these analyses can identify hot spot amino acids can serve target sites mutations. multiple sequence alignment utilizes data bases such prefab, sabmark, oxbench, irmbase, , balibase in order cross reference target protein sequences known sequences. multiple sequence alignment techniques listed below.

this method begins performing pair wise alignment of sequences using k-tuple or needleman–wunsch methods. these methods calculate matrix depicts pair wise similarity among sequence pairs. similarity scores transformed distance scores used produce guide tree using neighbor joining method. guide tree employed yield multiple sequence alignment.

clustal omega

this method capable of aligning 190,00 sequences utilizing k-tuple method. next sequences clustered using mbed , k-means methods. guide tree constructed using upgma method used hh align package. guide tree used generate multiple sequence alignments.

mafft

this method utilizes fast fourier transform (fft) converts amino acid sequences sequence composed of volume , polarity values each amino acid residue. new sequence used find homologous regions.

k-align

this method utilizes wu-manber approximate string matching algorithm generate multiple sequence alignments.

multiple sequence comparison log expectation (muscle)

this method utilizes kmer , kimura distances generate multiple sequence alignments.

t-coffee

this method utilizes tree based consistency objective functions alignment evolution. method has been shown 5-10% more accurate clustal w.