USING PROFILE HIDDEN MARKOV MODELS IN MULTIPLE SEQUENCE ALIGNMENT

Edi Edi

Abstract


Sequence alignment is a method of arranging sequences of DNA, RNA, or protein to identify similar regions between the sequences. Profile HMM is a type of HMM that can be used to construct family structure of multiple sequence alignment so that it can be used as a database for aligning or finding other sequences in that family. Literature review used as a method in this paper. Softwares BioEdit and HMMER are introduced.

Full Text:

PDF

References


A. Krogh, Computational Methods in

Molecular Biology edited by S.L.Salzberg, D. B. Searls and S. Kasif, pp.45-63, Elsevier, 1998.

V.D.Fonzo, F. Aluffi-Pentini,and V.Parisi, “Hidden Markov Models in Bioinformatics”, Current Bioinformatics, vol. 2, no. 1, pp. 49-61, 2007.

T. Nguyen, A. Khosravi, D. Creighton, and S. Nahavandi. "Hidden Markov models for cancer classification using gene expression profiles", Information Sciences, vol. 316, pp. 293-307, 2015.

K. H. Choo, J. C. Tong, and L. Zhang, “Recent Applications of Hidden Markov Models in Computational Biology”, Geno. Prot. Bioinfo., vol. 2, no. 2, pp. 84-96, 2004.

S. R. Eddy, ”Profile hidden Markov models”, Bioinformatics Review, vol.14, no.9, pp. 755-763, 1998.

Websites:

N. Mimouni, G. Lunter, C. Deane, Hidden Markov Models for Protein Sequence Alignment. https://www.stats.ox.ac.uk/__data/assets/file/0012/3360/naila_report.pdf.

Anonymous, Multiple Sequence Alignment, www.srmuniv.ac.in/sites/default/files/files/1(7).pdf.

Anonymous, Difference between Pairwise and Multiple Sequence Alignment. http://www.majordifferences.com/2016/05/difference-between-pairwise-and-multiple-sequence-alignment.html#.V9ZpTaJUXCs.

Clemens Gropl et al., Multiple Sequence Alignment, www.mi.fu-berlin.de/.../MultipleAlignmentWS12/multal.pdf, 2012.


Refbacks

  • There are currently no refbacks.