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PSTAG - Home

This software provides an implementation of the pair stochastic tree adjoining grammars (PSTAGs). For modeling 'pseudoknot' RNA structures, which is an extension of the pair hidden Markov models on tree structures (PHMMTSs). PSTAG is a novel method for structural alignment to align and predict RNA secondary structures including pseudoknots. By structural alignment, we mean a pairwise alignment to align "an unfolded RNA sequence" into "an RNA sequence of known secondary structure". Revised Sep 21, 2004.

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This software provides an implementation of the pair stochastic tree adjoining grammars (PSTAGs). For modeling 'pseudoknot' RNA structures, which is an extension of the pair hidden Markov models on tree structures (PHMMTSs). PSTAG is a novel method for structural alignment to align and predict RNA secondary structures including pseudoknots. By structural alignment, we mean a pairwise alignment to align an unfolded RNA sequence into an RNA sequence of known secondary structure. Revised Sep 21, 2004.
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PSTAG - Home | pstag.dna.bio.keio.ac.jp Reviews

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

This software provides an implementation of the pair stochastic tree adjoining grammars (PSTAGs). For modeling 'pseudoknot' RNA structures, which is an extension of the pair hidden Markov models on tree structures (PHMMTSs). PSTAG is a novel method for structural alignment to align and predict RNA secondary structures including pseudoknots. By structural alignment, we mean a pairwise alignment to align "an unfolded RNA sequence" into "an RNA sequence of known secondary structure". Revised Sep 21, 2004.

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PSTAG - Publications

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

Matsui, H, Sato, K. and Sakakibara, Y., Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures. Bioinformatics, vol.21, no.11, pp.2611-2617, 2005 [pubmed]. Revised Sep 21, 2004. Webmaster@dna.bio.keio.ac.jp.

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PSTAG - Download

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

PSTAG version 2.1.4a (10/Dec./2004). PSTAG version 2.1.2 (20/Sep./2004). Revised Sep 21, 2004. Webmaster@dna.bio.keio.ac.jp.

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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.

4

PSTAG - Home

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

This software provides an implementation of the pair stochastic tree adjoining grammars (PSTAGs). For modeling 'pseudoknot' RNA structures, which is an extension of the pair hidden Markov models on tree structures (PHMMTSs). PSTAG is a novel method for structural alignment to align and predict RNA secondary structures including pseudoknots. By structural alignment, we mean a pairwise alignment to align "an unfolded RNA sequence" into "an RNA sequence of known secondary structure". Revised Sep 21, 2004.

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Sakakibara Lab

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

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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).

ncrna.org ncrna.org

PSTAG – Bioinformatics Tools and Databases for Functional RNA Analysis

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

Pair Stochastic Tree Adjoining Grammars. PSTAG (Pair Stochastic Tree Adjoining Grammars) for RNA sequences including pseudoknotted structures. Matsui, H., Sato, K. and Sakakibara, Y.: Pair stcochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. Bioinformatics, 2005, 21, 2611-2617 [pubmed]. Http:/ pstag.dna.bio.keio.ac.jp/. NcRNA org is provided by Computational Biology Research Consortium.

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PSTAG - Home

This software provides an implementation of the pair stochastic tree adjoining grammars (PSTAGs). For modeling 'pseudoknot' RNA structures, which is an extension of the pair hidden Markov models on tree structures (PHMMTSs). PSTAG is a novel method for structural alignment to align and predict RNA secondary structures including pseudoknots. By structural alignment, we mean a pairwise alignment to align "an unfolded RNA sequence" into "an RNA sequence of known secondary structure". Revised Sep 21, 2004.

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