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my5C specifications

Information


Unique identifier OMICS_15677
Name my5C
Interface Web user interface
Restrictions to use None
Input data The 5C region file, the region name, the restriction site, the optimal primer length, the optimal TM, the primer set options, the primer pool description
Input format FASTA
Computer skills Basic
Stability No
Maintained No

Documentation


Maintainer


This tool is not available anymore.

Publication for my5C

my5C in publications

 (5)
PMCID: 5599062
PMID: 28863138
DOI: 10.1371/journal.pgen.1006966

[…] of the spatial chromatin looping contacts and identification of tads [, ]. for the 5c analysis, 381 forward and 382 reverse 5c probes were designed in an alternating scheme using the tools from my5c software suite [] to interrogate hindiii sites with the unique anchoring regions at the edc and its flanking regions (mm9, chromosome 3: 89.9–95.2 mbp) (, ). the designed probe pool interrogated […]

PMCID: 5290626
PMID: 28159004
DOI: 10.1186/s13059-017-1161-y

[…] provide robust and informative methods for the interpretation of hi-c data. here, we investigate five tools that can be operated using a web browser or a graphical user interface: hi-browse v1.6 [], my5c [], juicebox v1.5 [], the epigenome browser v40.6 [] and the 3d genome browser [] (table ). these tools do not require programming expertise, and are more readily accessible. we assess […]

PMCID: 4824072
PMID: 26615198
DOI: 10.1093/nar/gkv1300

[…] clustering of interaction frequencies., dhs and ctcf data sets for the saec (acc. no. gse26328 and gse30263) were downloaded from the geo website at http://www.ncbi.nlm.nih.gov/geo/query/acc. the ‘my5c-primer’ and ‘my5c-heatmap’ bioinformatics tools are found at http://3dg.umassmed.edu/my5cheatmap/heatmap.php., the published 5c data were obtained and visualized using the ucsc genome browser […]

PMCID: 3873244
PMID: 24385922
DOI: 10.1371/journal.pgen.1004018

[…] which do not contain ecori restriction sites. this analysis generates an excel sheet containing interaction frequency lists (ifl) as well as a text file, which was used to visualize results using ‘my5c-heatmap’ . limb-enriched 5c interactions were obtained by subtracting limb and head 5c-seq data. data was normalized by dividing the number of reads of each 5c contact by the total number […]

PMCID: 3555147
PMID: 22955621
DOI: 10.1038/nature11279

[…] (“distal fragments”) in the encode pilot regions., 5c primers were designed at hindiii restriction sites (aagctt) using 5c primer design tools previously developed and made available online at my5c website (http://my5c.umassmed.edu) . reverse 5c primers were designed for hindiii restriction fragments overlapping a known tss from gencode transcripts, or overlapping a start site […]


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my5C institution(s)
Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
my5C funding source(s)
This work was supported by The National Institutes of Health (HG003143, HG004592) and the Keck Foundation.

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