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BnS specifications

Information


Unique identifier OMICS_34147
Name BnS
Alternative name Bind-N-Seq
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS
Programming languages Perl
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline David Segal

Publication for Bind-N-Seq

BnS citations

 (11)
library_books

Dry and wet approaches for genome wide functional annotation of conventional and unconventional transcriptional activators

2016
Comput Struct Biotechnol J
PMCID: 4941109
PMID: 27453771
DOI: 10.1016/j.csbj.2016.06.004

[…] microarray-based techniques, many newly developed HT technologies have revolutionized the ability to characterize protein–DNA binding interactions. These additional technologies (listed in ) include: Bind-n-seq , EMSA-seq , HT-SELEX/SELEX-seq , and microarray-based investigation of genomic aptamers by shift (MEGAshift) . Despite their strikingly increased throughput compared to more basic methods […]

library_books

Deciphering the genomic targets of alkylating polyamide conjugates using high throughput sequencing

2016
Nucleic Acids Res
PMCID: 4872120
PMID: 27098039
DOI: 10.1093/nar/gkw283

[…] Bind-n-Seq experiments and high-throughput sequencing were performed based on our previous report (). Broadly, Synthesis of biotinylated alkylating PIPs and PIP-Conjugate 5 (a PIP conjugate where the […]

library_books

Protein Delivery of an Artificial Transcription Factor Restores Widespread Ube3a Expression in an Angelman Syndrome Mouse Brain

2016
PMCID: 4786922
PMID: 26727042
DOI: 10.1038/mt.2015.236

[…] ty of 5 ± 1.5 nmol/l (). The EMSA was repeated with the TAT-S1 and showed similar affinity of 8 ± 1.5 nmol/l (data not shown). The binding preference of the TAT-S1 was investigated using the in vitro Bind-n-seq assay, in which the protein was incubated with oligonucleotides representing all possible 21-bp binding regions, and the preferred targets were identified by next-generation sequencing. The […]

library_books

Miz 1 Activates Gene Expression via a Novel Consensus DNA Binding Motif

2014
PLoS One
PMCID: 4077741
PMID: 24983942
DOI: 10.1371/journal.pone.0101151

[…] nsensus DNA binding motifs is central to understanding the genomic binding of Miz-1 and its regulation of cellular biology.Using a maltose binding protein (MBP) fusion protein tag system, we employed Bind-n-Seq (BnS), an in vitro, high-throughput DNA binding assay with Multiple EM for Motif Elicitation (MEME) analysis to identify putative Miz-1 DNA biding motifs de novo. The BnS method is an effic […]

library_books

The prospect of molecular therapy for Angelman syndrome and other monogenic neurologic disorders

2014
BMC Neurosci
PMCID: 4069279
PMID: 24946931
DOI: 10.1186/1471-2202-15-76

[…] rget binding sites can be predicted to a large extent from in vitro and in vivo assays, making it possible to screen ATF candidates and select the most specific ones before human trials. For example, Bind-n-Seq and SELEX are methods to evaluate the most favored in vitro binding sites of an ATF from a random pool of all possible DNA targets []. Off-target sites can be predicted in silico based on s […]

library_books

Protein–DNA binding: complexities and multi protein codes

2013
Nucleic Acids Res
PMCID: 3936734
PMID: 24243859
DOI: 10.1093/nar/gkt1112

[…] es include: bacterial one-hybrid (B1H) (,), protein-binding microarrays (PBMs) (), total internal reflectance fluorescence-PBM (), mechanically induced trapping of molecular interactions (MITOMI) (), Bind-n-seq (), EMSA-seq (), HT-SELEX/SELEX-seq (), microarray evaluation of genomic aptamers by shift (MEGAshift) (), cognate site identifier (CSI) (), and HT sequencing fluorescent ligand interaction […]

Citations

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BnS institution(s)
Genome Center, University of California, Davis, CA, USA
BnS funding source(s)
Supported by the National Institutes of Health (GM077403).

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