Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models (Q24803400)

Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases

Europe PubMed Central

title

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models (English)

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James O McInerney

2

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author name string

Shaun Mahony

series ordinal

1

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Terry J Smith

series ordinal

3

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Aaron Golden

series ordinal

4

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language of work or name

English

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publication date

5 March 2004

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published in

BMC Bioinformatics

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volume

5

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issue

1

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page(s)

23

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cites work

1 reference

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Replicational and transcriptional selection on codon usage in Borrelia burgdorferi

7 April 2017

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7 April 2017

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Codon usage: mutational bias, translational selection, or both?

7 April 2017

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7 April 2017

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7 April 2017

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Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS

7 April 2017

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The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

7 April 2017

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7 April 2017

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Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi

7 April 2017

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The complete genome sequence of the gram-positive bacterium Bacillus subtilis

7 April 2017

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7 April 2017

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7 April 2017

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Improved microbial gene identification with GLIMMER

7 April 2017

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The complete genome sequence of Escherichia coli K-12

7 April 2017

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Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii

7 April 2017

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Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

7 April 2017

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Evolution of synonymous codon usage in metazoans

7 April 2017

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Genome Sequence of the Radioresistant Bacterium Deinococcus radiodurans R1

7 April 2017

1 reference

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The Minimal Gene Complement of Mycoplasma genitalium

7 April 2017

1 reference

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Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

7 April 2017

1 reference

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Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC6803. II. Sequence Determination of the Entire Genome and Assignment of Potential Protein-coding Regions

7 April 2017

1 reference

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

7 April 2017

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Asymmetric substitution patterns in the two DNA strands of bacteria

7 April 2017

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Informatics for unveiling hidden genome signatures

7 April 2017

1 reference

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Current methods of gene prediction, their strengths and weaknesses

28 September 2017

1 reference

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Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Selection at the amino acid level can influence synonymous codon usage: implications for the study of codon adaptation in plastid genes.

28 September 2017

1 reference

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An assessment of gene prediction accuracy in large DNA sequences

28 September 2017

1 reference

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Genome annotation assessment in Drosophila melanogaster

28 September 2017

1 reference

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Powers and pitfalls in sequence analysis: the 70% hurdle

28 September 2017

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Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes

28 September 2017

1 reference

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Strand compositional asymmetry in bacterial and large viral genomes

28 September 2017

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Detection of new genes in a bacterial genome using Markov models for three gene classes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

The selection-mutation-drift theory of synonymous codon usage

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Assessment of protein coding measures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Strand asymmetries in DNA evolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Improving gene recognition accuracy by combining predictions from two gene-finding programs.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Finding genes by computer: the state of the art.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Analysis of codon usage patterns of bacterial genomes using the self-organizing map.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Codon bias and base composition are poor indicators of horizontally transferred genes

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Gene prediction and gene classes in Arabidopsis thaliana

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

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

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=385221

Translation conditional models for protein coding sequences

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15070404

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-5-23

0 references

DBLP publication ID

journals/bmcbi/MahonyMSG04

1 reference

DBLP Dataset 2021-01-02