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PHMMTS - Home

This page provides an implementation of the pair hidden Markov models on tree structures (PHMMTSs). Which is an extension of the. Pair hidden Markov models (PHMMs. Defined on alignments of trees. PHMMTS provides a unifying framework and an automata-theoretic model for alignments of trees, structural alignments and pair stochastic context-free grammars. By structural alignment, we mean a pairwise alignment to align an unfolded RNA sequence into an RNA sequence of known secondary structure.

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PHMMTS - Home | phmmts.dna.bio.keio.ac.jp Reviews

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This page provides an implementation of the pair hidden Markov models on tree structures (PHMMTSs). Which is an extension of the. Pair hidden Markov models (PHMMs. Defined on alignments of trees. PHMMTS provides a unifying framework and an automata-theoretic model for alignments of trees, structural alignments and pair stochastic context-free grammars. By structural alignment, we mean a pairwise alignment to align an unfolded RNA sequence into an RNA sequence of known secondary structure.

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PHMMTS - Home | phmmts.dna.bio.keio.ac.jp Reviews

https://phmmts.dna.bio.keio.ac.jp

This page provides an implementation of the pair hidden Markov models on tree structures (PHMMTSs). Which is an extension of the. Pair hidden Markov models (PHMMs. Defined on alignments of trees. PHMMTS provides a unifying framework and an automata-theoretic model for alignments of trees, structural alignments and pair stochastic context-free grammars. By structural alignment, we mean a pairwise alignment to align an unfolded RNA sequence into an RNA sequence of known secondary structure.

LINKS TO THIS WEBSITE

dna.bio.keio.ac.jp

Sakakibara Lab

http://www.dna.bio.keio.ac.jp/index.html

dna.bio.keio.ac.jp

Software - Sakakibara Lab

http://www.dna.bio.keio.ac.jp/software.html

Software - Sakakibara Lab. ゲノム配列から，アンカーと呼ばれる数十数百塩基程度の比較的短い相同領域を高速に検出するソフトウェアです 3 本以上の配列を同時に扱えることと，ヒトの染色体のような長い配列を扱えることが特徴です. Murasakiなどのゲノム比較ツールによって計算されたアンカーを入力としますそして，比較している生物種の中で，ゲノム再編成が起こっていない領域遺伝子の並びが変化していない領域を同定するプログラムです. RNA 配列のアラインメントと 2 次構造を計算するプログラムです 2 次構造未知の入力配列を 2 次構造既知の参照配列に対してアラインメントします. RNA 配列のアラインメントと 2 次構造を計算するプログラムです PHMMTS の拡張版であり，シュードノットと呼ばれる特殊な 2 次構造を扱うことができます. RNA 配列間の類似度を極めて正確に計算するプログラムですこれまでに機能性 RNA のファミリ予測，クラスタリング，プロファイル探索，相同性検索など様々な解析に応用され，いずれも世界最高の精度を達成しています (2010年11月現在).

pstag.dna.bio.keio.ac.jp

PSTAG - Link

http://pstag.dna.bio.keio.ac.jp/link.html

Pair Hidden Markov Models on Tree Structures. The department of Biosciences and Informatics, Keio University Faculty of Science and Technology. Revised Sep 21, 2004. Webmaster@dna.bio.keio.ac.jp.

ncrna.org

PHMMTS – Bioinformatics Tools and Databases for Functional RNA Analysis

https://www.ncrna.org/softwares/phmmts

Pair Hidden Markov Models on Tree Structures. PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure. Sakakibara, Y: Pair hidden Markov models on tree structures. Bioinformatics, 2003, 19 Supl 1, i232-240 [pubmed]. Sato, K. and Sakakibara, Y.: RNA secondary structural alignment with conditional random fields. Bioinformatics, 2005, 21 Suppl 2, ii237-ii242 [pubmed].

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PHMMTS - Home

This page provides an implementation of the pair hidden Markov models on tree structures (PHMMTSs). Which is an extension of the. Pair hidden Markov models (PHMMs. Defined on alignments of trees. PHMMTS provides a unifying framework and an automata-theoretic model for alignments of trees, structural alignments and pair stochastic context-free grammars. By structural alignment, we mean a pairwise alignment to align an unfolded RNA sequence into an RNA sequence of known secondary structure.

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