Complexity of comparing hidden markov models

Autor: Christian N. S. Pedersen, Rune B. Lyngsø

Publikováno v: Algorithms and Computation ISBN: 9783540429852
ISAAC
Lyngsø, R B, Pedersen, C N S, Eades, P (ed.) & Takaoka, T (ed.) 2001, Complexity of Comparing Hidden Markov Models . in Ikke angivet . 2223 of Lecture Notes in Computer Science edn, Springer, pp. 416-428, Christchurch, New Zealand, 19/12/2001 .

The basic theory of hidden Markov models was developed and applied to problems in speech recognition in the late 1960's, and has since then been applied to numerous problems, e.g. biological sequence analysis. In this paper we consider the problem of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9ff4f6d83a78e17c388fa7cf9ec1e46a
https://doi.org/10.1007/3-540-45678-3_36

Stochastic models of sequence evolution including insertion—deletion events

Autor: Adam M. Novak, István Miklós, Rahul Satija, Jotun Hein, Rune B. Lyngsø

Publikováno v: Statistical Methods in Medical Research. 18:453-485

Comparison of sequences that have descended from a common an- cestor based on an explicit stochastic model of substitutions, insertions an d dele- tions has risen to prominence in the last decade. Making statements about the positions of insertions-d

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::172b0d9bde613dfe781a1068c985210e
https://doi.org/10.1177/0962280208099500

RNA Secondary Structure Prediction Including Pseudoknots

Autor: Rune B. Lyngsø

Publikováno v: Encyclopedia of Algorithms ISBN: 9783642278488

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c98f348a14bc8587f79521fbe529a6b2
https://doi.org/10.1007/978-3-642-27848-8_346-2

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

Autor: Jakob Hull Havgaard, Jan Gorodkin, Rune B. Lyngsø

Publikováno v: Nucleic Acids Research

Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of foldalign. The server can be used

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6edbf0c4b96cc2e841b9101c2a579291
https://doi.org/10.1093/nar/gki473

SCFGs in RNA Secondary Structure Prediction: A Hands-on Approach

Autor: Zsuzsanna Sükösd, Ebbe Sloth Andersen, Rune B. Lyngsø

Publikováno v: Methods in Molecular Biology ISBN: 9781627037082

Stochastic context-free grammars (SCFGs) were first established in the context of natural language modelling, and only later found their applications in RNA secondary structure prediction. In this chapter, we discuss the basic SCFG algorithms (CYK an

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a5c8feb03e805d166d0f411b397472d5
https://doi.org/10.1007/978-1-62703-709-9_8