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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

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This tool is not maintained anymore.

Publication for Kismeth

Kismeth citations

 (49)
library_books

CRISPR/Cas9 mediated gene targeting in Arabidopsis using sequential transformation

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

[…] 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., the authors declare that all the data supporting the findings of this study are available within the paper and its supplementary information files. the data sets generated or analyzed […]

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. , for whole‐genome bisulfite sequencing data extraction, raw data from a previously published study of 1 atherosclerotic (grade vii)/normal human aortic tissue pair was downloaded […]

library_books

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

2017
PMCID: 5724284
PMID: 29158416
DOI: 10.1073/pnas.1716459114

[…] 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 ()., genomic dnas (1–3 μg) isolated from nb, eg4, and a119 seedlings using the dneasy plant mini kit (qiagen) were sheared with a covaris instrument to mean size of 300 bp. fragments […]

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)., the raw data files obtained in this study by illumina sequencing have been released in the sequence read archive database of the national center […]

library_books

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

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

[…] 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., the ppd-b1 gene copy number in the f2 population and both parents was determined by idna genetics (norwich, […]

library_books

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

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

[…] 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 […]


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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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