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PSTAG specifications

Information


Unique identifier OMICS_21231
Name PSTAG
Alternative name Pair Stochastic Tree Adjoining Grammars
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

Maintainer


This tool is not maintained anymore.

Information


Unique identifier OMICS_21231
Name PSTAG
Alternative name Pair Stochastic Tree Adjoining Grammars
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Version 2.1.4a
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yasubumi Sakakibara

Publication for Pair Stochastic Tree Adjoining Grammars

PSTAG citations

 (4)
library_books

Combined Overlap Extension PCR Method for Improved Site Directed Mutagenesis

2016
Biomed Res Int
PMCID: 5138438
PMID: 27995143
DOI: 10.1155/2016/8041532

[…]  pmol GSP, 1.25 pmol MP, 2 U Pfu DNA polymerase (Fermentas), 5 nmol dNTP mix, 62.5 nmol MgCl2, and 2.5 pg template DNA in a 25 μL reaction. The template was the Stisa2 gene (Accession: AY132997) in a pSTAG vector [, ]. The PCR thermocycling profile used was as follows: initial denaturation for 5 minutes at 95°C, followed by 30 cycles of 30 seconds at 94°C, 30 seconds at annealing temperature, and […]

library_books

Hidden Markov Models and their Applications in Biological Sequence Analysis

2009
Curr Genomics
PMCID: 2766791
PMID: 20190955
DOI: 10.2174/138920209789177575

[…] al alignment is distinct from a sequence-based alignment, in the sense that we consider both the structural similarity and the sequence similarity when finding the optimal alignment between the RNAs. Pair stochastic tree adjoining grammars (PSTAGs) extend the PHMMTSs further, so that we can use them to align TAG (tree adjoining grammar) trees []. This extension allows us to align RNAs with more co […]

library_books

Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints

2009
EURASIP J Bioinform Syst Biol
PMCID: 3171428
PMID: 19390684
DOI: 10.1155/2009/491074

[…] accuracy. We can also note that the PSTAG-based alignment takes considerably longer than the profile-csHMM-based alignment. The large difference in alignment speed is mainly due to the fact that the PSTAG algorithm [] does not incorporate any constraint to restrict the alignment space.It would be also interesting to see how the parameters used for predicting the alignment constraint would affect […]

library_books

Software.ncrna.org: web servers for analyses of RNA sequences

2008
Nucleic Acids Res
PMCID: 2447773
PMID: 18440970
DOI: 10.1093/nar/gkn222

[…] equence analyses based on common potential secondary structures: pairwise alignment, multiple alignment and structural motif extraction. SCARNA, PHMMTS (pair hidden Markov models on tree structures), PSTAG (pair stochastic tree adjoining grammar), Murlet and MXSCARNA can be used on their stand-alone web servers as well as on our integrated server. In addition, the source codes for PHMMTS, PSTAG, M […]

Citations

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PSTAG institution(s)
Keio University, Department of Biosciences and Informatics, Yokohama, Japan

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