(Q33317617)

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SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

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scholarly article

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Europe PubMed Central

25 July 2017

SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics (English)

1 reference

Europe PubMed Central

25 July 2017

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4

object named as

Bertrand Aigle

1 reference

Europe PubMed Central

25 July 2017

Fabrice Touzain

object named as

Fabrice Touzain

1

0 references

object named as

Pierre Leblond

6

0 references

Gregory Kucherov

object named as

Gregory Kucherov

5

0 references

author name string

Sophie Schbath

2

1 reference

Europe PubMed Central

25 July 2017

Isabelle Debled-Rennesson

3

1 reference

Europe PubMed Central

25 July 2017

publication date

31 January 2008

1 reference

Europe PubMed Central

25 July 2017

BMC Bioinformatics

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Europe PubMed Central

25 July 2017

9

1 reference

Europe PubMed Central

25 July 2017

73

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Europe PubMed Central

25 July 2017

copyright license

Creative Commons Attribution 2.0 Generic

31 January 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

1 reference

April 2022 Public Data File from Crossref

https://scigraph.springernature.com/pub.10.1186/1471-2105-9-73

0 references

Statistical tests to compare motif count exceptionalities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Mycobacterial transcriptional signals: requirements for recognition by RNA polymerase and optimal transcriptional activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

The structural basis for promoter -35 element recognition by the group IV sigma factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Assessing computational tools for the discovery of transcription factor binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

The Complete Genome Sequence of Bacillus licheniformis DSM13, an Organism with Great Industrial Potential

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Trends between gene content and genome size in prokaryotic species with larger genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Genome wide identification of regulatory motifs in Bacillus subtilis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

MBGD: microbial genome database for comparative analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Identification of the binding sites of regulatory proteins in bacterial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Finding motifs using random projections

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

The EcoCyc Database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Complete genome sequence of Salmonella enterica serovar Typhimurium LT2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

The alternative sigma factor SigH regulates major components of oxidative and heat stress responses in Mycobacterium tuberculosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

BldD is a direct regulator of key developmental genes in Streptomyces coelicolor A3(2).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Generation of a non-sporulating strain of Streptomyces coelicolor A3(2) by the manipulation of a developmentally controlled ftsZ promoter

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Combinatorial approaches to finding subtle signals in DNA sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

sigma(BldN), an extracytoplasmic function RNA polymerase sigma factor required for aerial mycelium formation in Streptomyces coelicolor A3(2).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Regulation of the furA and catC operon, encoding a ferric uptake regulator homologue and catalase-peroxidase, respectively, in Streptomyces coelicolor A3(2).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Prediction of transcription regulatory sites in Archaea by a comparative genomic approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Eubacterial sigma-factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

The Streptomyces coelicolor sporulation-specific sigma WhiG form of RNA polymerase transcribes a gene encoding a ProX-like protein that is dispensable for sporulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

The bldB gene encodes a small protein required for morphogenesis, antibiotic production, and catabolite control in Streptomyces coelicolor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

The complete genome sequence of Escherichia coli K-12

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

An efficient statistic to detect over- and under-represented words in DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Identification of sigma factors for growth phase-related promoter selectivity of RNA polymerases from Streptomyces coelicolor A3(2)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Escherichia coli promoter sequences: analysis and prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Gibbs motif sampling: detection of bacterial outer membrane protein repeats

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Compilation of E. coli mRNA promoter sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Compilation and analysis ofEscherichia colipromoter DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Analysis of E. coli promoter sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Two promoters from the Streptomyces plasmid pIJ101 and their expression in Escherichia coli.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Compilation and analysis of DNA sequences associated with apparent streptomycete promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Direct repeat sequences are implicated in the regulation of two Streptomyces chitinase promoters that are subject to carbon catabolite control

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

Isolation and characterization of the major vegetative RNA polymerase of Streptomyces coelicolor A3(2); renaturation of a sigma subunit using GroEL.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

21 June 2018

An efficient algorithm for the identification of structured motifs in DNA promoter sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Promoter prediction in the rhizobia.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Transcriptional analysis of the recA gene in Streptomyces rimosus: identification of the new type of promoter.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Defining the disulphide stress response in Streptomyces coelicolor A3(2): identification of the sigmaR regulon.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

SigB, an RNA polymerase sigma factor required for osmoprotection and proper differentiation of Streptomyces coelicolor.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Numerical comparison of several approximations of the word count distribution in random sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375139

31 October 2018

Transcriptional co-regulation of five chitinase genes scattered on the Streptomyces coelicolor A3(2) chromosome

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237374

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237374

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifying target sites for cooperatively binding factors

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237374

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomyces coelicolor A3(2)

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237374

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237374

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome-wide analysis of bacterial promoter regions

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237374

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1471-2105-9-73

1 reference

Europe PubMed Central

25 July 2017

DBLP publication ID

journals/bmcbi/TouzainSDAKL08

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

1 reference

Europe PubMed Central

25 July 2017

1 reference

Europe PubMed Central

25 July 2017

ResearchGate publication ID

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