(Q34722882)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Sacha van Hijum

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

author name string

Lex Overmars

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

language of work or name

English

0 references

publication date

10 May 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

volume

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

page(s)

e63523

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

1 March 2020

copyright license

start time

10 May 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The automatic annotation of bacterial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Genome majority vote improves gene predictions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

The Pfam protein families database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Genome (re-)annotation and open-source annotation pipelines

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Combining gene prediction methods to improve metagenomic gene annotation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Benchmarking of gene prediction programs for metagenomic data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Prodigal: prokaryotic gene recognition and translation initiation site identification

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

FIGfams: yet another set of protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Evaluation of three automated genome annotations for Halorhabdus utahensis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Application of 'next-generation' sequencing technologies to microbial genetics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

NCBI Reference Sequences: current status, policy and new initiatives

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

The RAST Server: rapid annotations using subsystems technology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Advanced sequencing technologies and their wider impact in microbiology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Identifying bacterial genes and endosymbiont DNA with Glimmer

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

xBASE, a collection of online databases for bacterial comparative genomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

BASys: a web server for automated bacterial genome annotation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

The Universal Protein Resource (UniProt)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

The complete genome and proteome of Mycoplasma mobile

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

GeneComber: combining outputs of gene prediction programs for improved results

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

DAVID: Database for Annotation, Visualization, and Integrated Discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Complete Genome Sequence of Neisseria meningitidis Serogroup B Strain MC58

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Improved microbial gene identification with GLIMMER

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

A genomic perspective on protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Basic local alignment search tool

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

A Bayesian framework for combining gene predictions

7 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0063523

xBASE2: a comprehensive resource for comparative bacterial genomics.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0063523

DIGIT: a novel gene finding program by combining gene-finders.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3651085

Errors in genome annotation

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23675487

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

An Ergatis-based prokaryotic genome annotation web server

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23675487

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0063523

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

PubMed publication ID

23675487

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675487%20AND%20SRC:MED&resulttype=core&format=json