USING PROFILE HIDDEN MARKOV MODELS IN MULTIPLE SEQUENCE ALIGNMENT

Isi Artikel Utama

Edi Edi

Abstrak

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.

Rincian Artikel

Cara Mengutip
[1]
E. Edi, “USING PROFILE HIDDEN MARKOV MODELS IN MULTIPLE SEQUENCE ALIGNMENT”, JTM, vol. 5, no. 2, hlm. 55–57, Feb 2017.
Bagian
Articles

Referensi

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 Bioinformaticsâ€, 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 Biologyâ€, Geno. Prot. Bioinfo., vol. 2, no. 2, pp. 84-96, 2004.

S. R. Eddy, â€Profile hidden Markov modelsâ€, 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.