(Q35570198)

8 August 2017

title

An integrative method for identifying the over-annotated protein-coding genes in microbial genomes (English)

1 reference

8 August 2017

Jia-Feng Yu

1

1 reference

8 August 2017

Ke Xiao

2

1 reference

8 August 2017

Dong-Ke Jiang

3

1 reference

8 August 2017

Jing Guo

4

1 reference

8 August 2017

Ji-Hua Wang

5

1 reference

8 August 2017

Xiao Sun

6

1 reference

8 August 2017

publication date

8 September 2011

1 reference

8 August 2017

1 reference

8 August 2017

volume

18

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8 August 2017

issue

6

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8 August 2017

page(s)

435-449

1 reference

Using comparative genome analysis to identify problems in annotated microbial genomes.

8 August 2017

cites work

1 reference

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27 July 2018

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27 July 2018

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Evaluation of three automated genome annotations for Halorhabdus utahensis

27 July 2018

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Identify protein-coding genes in the genomes of Aeropyrum pernix K1 and Chlorobium tepidum TLS.

27 July 2018

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27 July 2018

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Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

27 July 2018

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Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

27 July 2018

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Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses

27 July 2018

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Detecting laterally transferred genes: use of entropic clustering methods and genome position

27 July 2018

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Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence

27 July 2018

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Genetic flux over time in the Salmonella lineage

27 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Estimating the annotation error rate of curated GO database sequence annotations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Genome re-annotation: a wiki solution?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

27 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Do different surrogate methods detect lateral genetic transfer events of different relative ages?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Large-scale prokaryotic gene prediction and comparison to genome annotation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Genome Update: annotation quality in sequenced microbial genomes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Comparison of various algorithms for recognizing short coding sequences of human genes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

NCBI Reference Sequence project: update and current status

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

The past, present and future of genome-wide re-annotation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Intrinsic errors in genome annotation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Computational methods for gene annotation: the Arabidopsis genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Horizontal gene transfer in bacterial and archaeal complete genomes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

The COG database: a tool for genome-scale analysis of protein functions and evolution

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Improved microbial gene identification with GLIMMER

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

GeneMark.hmm: new solutions for gene finding

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

The guanine and cytosine content of genomic DNA and bacterial evolution

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Analysis of distribution of bases in the coding sequences by a diagrammatic technique

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Assessment of protein coding measures

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Reannotation of protein-coding genes based on an improved graphical representation of DNA sequence.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Re-prediction of protein-coding genes in the genome of Amsacta moorei entomopoxvirus

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Using purine skews to predict genes in AT-rich poxviruses

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Development of joint application strategies for two microbial gene finders

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

YACOP: Enhanced gene prediction obtained by a combination of existing methods.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Gene recognition from questionable ORFs in bacterial and archaeal genomes.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

On the total number of genes and their length distribution in complete microbial genomes

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Studies on the relationships between the synonymous codon usage and protein secondary structural units

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Evaluation of gene structure prediction programs.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223076

Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes

26 September 2018

1 reference

12 December 2020

The evolution of base composition and phylogenetic inference

1 reference

12 December 2020

Errors in genome annotation

1 reference

12 December 2020

TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications

1 reference

12 December 2020

H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences

1 reference

12 December 2020

Identification of protein-coding genes in the genome of Vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotides

1 reference

12 December 2020

Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code

1 reference

12 December 2020

Identifiers

DOI

10.1093/DNARES/DSR030

1 reference

8 August 2017

1 reference

8 August 2017

1 reference