VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data (Q34222990)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22480257%20AND%20SRC:MED&resulttype=core&format=json

28 January 2020

title

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data (English)

1 reference

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28 January 2020

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0 references

2

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28 January 2020

Samuel H Payne

8

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28 January 2020

Joshua N Adkins

10

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28 January 2020

William R. Cannon

11

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28 January 2020

Bobbie-Jo Webb-Robertson

12

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28 January 2020

author name string

Elena S Peterson

1

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28 January 2020

Alexandra C Schrimpe-Rutledge

3

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28 January 2020

Jeffrey L Jensen

4

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28 January 2020

Hyunjoo Walker

5

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28 January 2020

Markus A Kobold

6

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28 January 2020

Samantha R Webb

7

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28 January 2020

Charles Ansong

9

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28 January 2020

language of work or name

English

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publication date

5 April 2012

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28 January 2020

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28 January 2020

volume

13

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28 January 2020

page(s)

131

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Comparative omics-driven genome annotation refinement: application across Yersiniae

28 January 2020

cites work

1 reference

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Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA

5 July 2018

1 reference

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OryzaPG-DB: rice proteome database based on shotgun proteogenomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Large improvements in MS/MS-based peptide identification rates using a hybrid analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Identification, variation and transcription of pneumococcal repeat sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Integrative genomics viewer

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

A proteogenomic update to Yersinia: enhancing genome annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Proteogenomics to discover the full coding content of genomes: a computational perspective

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Proteogenomics and systems biology: quest for the ultimate missing parts

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

A guided tour of the Trans-Proteomic Pipeline

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Tablet--next generation sequence assembly visualization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Integrating multiple 'omics' analysis for microbial biology: application and methodologies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

MSQuant, an open source platform for mass spectrometry-based quantitative proteomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

JBrowse: a next-generation genome browser

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

The Sequence Alignment/Map format and SAMtools

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Apical loop-internal loop RNA pseudoknots: a new type of stimulator of -1 translational frameshifting in bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

DAnTE: a statistical tool for quantitative analysis of -omics data.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Proteogenomics: needs and roles to be filled by proteomics in genome annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Integrated data analysis for genome-wide research

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Gbrowse Moby: a Web-based browser for BioMoby Services

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Comparison of probability and likelihood models for peptide identification from tandem mass spectrometry data.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Artemis: sequence visualization and annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

QVALITY: non-parametric estimation of q-values and posterior error probabilities

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3364912

WebGBrowse--a web server for GBrowse

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22480257

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-13-131

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22480257%20AND%20SRC:MED&resulttype=core&format=json

28 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22480257%20AND%20SRC:MED&resulttype=core&format=json

28 January 2020

PubMed publication ID

22480257

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22480257%20AND%20SRC:MED&resulttype=core&format=json