CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model (Q39596956)

13 September 2017

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model (English)

1 reference

logistic regression model

13 September 2017

1 reference

Liguo Wang

1 reference

13 September 2017

Hyun Jung Park

1 reference

13 September 2017

Surendra Dasari

1 reference

13 September 2017

Shengqin Wang

1 reference

13 September 2017

Jean-Pierre Kocher

1 reference

13 September 2017

Wei Li

1 reference

13 September 2017

language of work or name

English

0 references

publication date

17 January 2013

1 reference

13 September 2017

Nucleic Acids Research

1 reference

13 September 2017

1 reference

13 September 2017

1 reference

13 September 2017

e74

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

13 September 2017

start time

12 May 2017

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Non-coding RNAs as regulators of embryogenesis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Long noncoding RNA in genome regulation: prospects and mechanisms

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Long noncoding RNAs with enhancer-like function in human cells

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Differentiating protein-coding and noncoding RNA: challenges and ambiguities

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

RNA maps reveal new RNA classes and a possible function for pervasive transcription

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

The transcriptional landscape of the mammalian genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

ROCR: visualizing classifier performance in R

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Global identification of human transcribed sequences with genome tiling arrays

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Recognition of protein coding regions in DNA sequences

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Assessment of protein coding measures

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

Discrimination of non-protein-coding transcripts from protein-coding mRNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3616698

17 June 2018

Identifiers

DOI

10.1093/NAR/GKT006

1 reference

13 September 2017

1 reference

13 September 2017

PubMed publication ID

23335781

1 reference