(Q40800225)

23 September 2017

Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations (English)

1 reference

23 September 2017

Poonam Singhal

1

1 reference

23 September 2017

B Jayaram

series ordinal

2

1 reference

23 September 2017

Surjit B Dixit

series ordinal

3

1 reference

23 September 2017

David L Beveridge

series ordinal

4

1 reference

23 September 2017

language of work or name

English

0 references

publication date

7 March 2008

1 reference

23 September 2017

11

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

23 September 2017

94

1 reference

23 September 2017

11

1 reference

23 September 2017

4173-4183

1 reference

Ten years of bacterial genome sequencing: comparative-genomics-based discoveries.

23 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

How sequence defines structure: a crystallographic map of DNA structure and conformation.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Current methods of gene prediction, their strengths and weaknesses

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Computational prediction of eukaryotic protein-coding genes

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Gene-finding approaches for eukaryotes

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

EcoGene: a genome sequence database for Escherichia coli K-12.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Improved microbial gene identification with GLIMMER

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Heuristic approach to deriving models for gene finding

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Bacterial start site prediction

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Self-identification of protein-coding regions in microbial genomes.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

GeneMark.hmm: new solutions for gene finding

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Microbial gene identification using interpolated Markov models

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

A hidden Markov model that finds genes in E. coli DNA

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

On the convergence of a clustering algorithm for protein-coding regions in microbial genomes

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Computational methods for the identification of genes in vertebrate genomic sequences.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Perceptron-based learning algorithms.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

The gene identification problem: an overview for developers

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

A physicochemical model for analyzing DNA sequences.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

A novel bacterial gene-finding system with improved accuracy in locating start codons

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

How to interpret an anonymous bacterial genome: machine learning approach to gene identification.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480686

Beyond the wobble: the rule of conjugates

19 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18326660

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Root mean square deviation probability analysis of molecular dynamics trajectories on DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18326660

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1529/BIOPHYSJ.107.116392

1 reference

23 September 2017

1 reference

23 September 2017

PubMed publication ID

18326660

1 reference