Hidden Markov model: Difference between revisions

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== Applications ==

[[File:A profile HMM modelling a multiple sequence alignment.png|thumb|right|A profile HMM modelling a multiple sequence alignment of proteins in [[Pfam]]]]

HMMs can be applied in many fields where the goal is to recover a data sequence that is not immediately observable (but other data that depend on the sequence are). Applications include:

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* Sequence classification<ref>{{Cite journal |last1=Blasiak |first1=S. |last2=Rangwala |first2=H. |title=A Hidden Markov Model Variant for Sequence Classification |journal=IJCAI Proceedings-International Joint Conference on Artificial Intelligence |volume=22 |pages=1192 |year=2011 }}</ref>

* [[Metamorphic virus detection]]<ref>{{Cite journal |last1=Wong |first1=W. |last2=Stamp |first2=M. |doi=10.1007/s11416-006-0028-7 |title=Hunting for metamorphic engines |journal=Journal in Computer Virology |volume=2 |issue=3 |pages=211–229 |year=2006 |s2cid=8116065 }}</ref>

* [[sequenceSequence motif|]] discovery (DNA motifand discovery]]proteins)<ref>{{Cite journal |last1=Wong |first1=K. -C. |last2=Chan |first2=T. -M. |last3=Peng |first3=C. |last4=Li |first4=Y. |last5=Zhang |first5=Z. |title=DNA motif elucidation using belief propagation |doi=10.1093/nar/gkt574 |journal=Nucleic Acids Research |volume=41 |issue=16 |pages=e153 |year=2013 |pmid=23814189 |pmc=3763557}}</ref>

* DNA hybridization kinetics<ref>{{Cite journal|last1=Shah|first1=Shalin|last2=Dubey|first2=Abhishek K.|last3=Reif|first3=John|date=2019-05-17|title=Improved Optical Multiplexing with Temporal DNA Barcodes|journal=ACS Synthetic Biology|volume=8|issue=5|pages=1100–1111|doi=10.1021/acssynbio.9b00010|pmid=30951289|s2cid=96448257}}</ref><ref>{{Cite journal|last1=Shah|first1=Shalin|last2=Dubey|first2=Abhishek K.|last3=Reif|first3=John|date=2019-04-10|title=Programming Temporal DNA Barcodes for Single-Molecule Fingerprinting|journal=Nano Letters|volume=19|issue=4|pages=2668–2673|doi=10.1021/acs.nanolett.9b00590|pmid=30896178|bibcode=2019NanoL..19.2668S|s2cid=84841635|issn=1530-6984}}</ref>

*[[Chromatin]] state discovery<ref>{{Cite web|url=http://compbio.mit.edu/ChromHMM/|title=ChromHMM: Chromatin state discovery and characterization|website=compbio.mit.edu|access-date=2018-08-01}}</ref>