Kismeth statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Kismeth
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Tool usage distribution map

This map represents all the scientific publications referring to Kismeth per scientific context
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Associated diseases

This word cloud represents Kismeth usage per disease context
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Protocols

Kismeth specifications

Information


Unique identifier OMICS_00602
Name Kismeth
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not maintained anymore.

Publication for Kismeth

Kismeth citations

 (51)
library_books

CRISPR/Cas9 mediated gene targeting in Arabidopsis using sequential transformation

2018
Nat Commun
PMCID: 5958078
PMID: 29773790
DOI: 10.1038/s41467-018-04416-0

[…] e amplified by specific primers (Supplementary Table ), then the amplicons were cloned into pMD-18 (Takara), and at least 27 independent colonies were sequenced. The sequence results were analyzed by Kismeth. […]

library_books

Liver X Receptor–Binding DNA Motif Associated With Atherosclerosis‐Specific DNA Methylation Profiles of Alu Elements and Neighboring CpG Islands

2018
PMCID: 5850253
PMID: 29386205
DOI: 10.1161/JAHA.117.007686

[…] was treated with sodium bisulfite using the EZ DNA Methylation‐Gold system (Zymo). PCR products obtained with the gene‐specific primers listed in Table  were cloned, sequenced, and analyzed with the Kismeth software. […]

library_books

Tracking the genome wide outcomes of a transposable element burst over decades of amplification

2017
Proc Natl Acad Sci U S A
PMCID: 5724284
PMID: 29158416
DOI: 10.1073/pnas.1716459114

[…] quick gel extraction kit (Qiagen) and were cloned with the TOPO TA cloning kit (Invitrogen). For each sample, 10–20 independent colonies were selected and sequenced, and sequences were analyzed using Kismeth software (). […]

library_books

Genome Wide Analysis of DNA Methylation During Ovule Development of Female Sterile Rice fsv1

2017
PMCID: 5677159
PMID: 28877971
DOI: 10.1534/g3.117.300243

[…] and CHH, and were calculated by dividing the number of nonconverted cytosines by the total number of cytosines within the assay. Analyses of the bisulfite sequencing results were conducted using the Kismeth website (http://katahdin.mssm.edu/kismeth). […]

library_books

Heritable heading time variation in wheat lines with the same number of Ppd B1 gene copies

2017
PLoS One
PMCID: 5573275
PMID: 28846721
DOI: 10.1371/journal.pone.0183745

[…] ducts were purified and sequenced as previously described []. The sequences were trimmed and aligned using Geneious 5.6.4 (http://www.geneious.com, []). The methylation status was determined with the Kismeth online tool, which is available at http://katahdin.mssm.edu/kismeth/revpage.pl. […]

library_books

Genome wide comparative analysis of DNA methylation between soybean cytoplasmic male sterile line NJCMS5A and its maintainer NJCMS5B

2017
BMC Genomics
PMCID: 5557475
PMID: 28806912
DOI: 10.1186/s12864-017-3962-5

[…] r of loci []. Twenty-five DMRs were selected randomly to validate the reliability of the sequencing data using a nest PCR (nPCR). All the primers (Additional file ) were designed using the website of Kismeth (http://katahdin.mssm.edu/kismeth/revpage.pl), and synthesized commercially (Invitrogen, Shanghai, China). Briefly, 1 μg of genomic DNA was treated by bisulfite according to the protocol of th […]


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Kismeth institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; National Institute of Biological Sciences, Beijing, No, Zhongguancun Life Science Park, Beijing, China; Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, USA

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