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Citations per year

Number of citations per year for the bioinformatics software tool MethBLAST
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Protocols

MethBLAST specifications

Information


Unique identifier OMICS_26654
Name MethBLAST
Interface Web user interface
Restrictions to use None
Input data Some primer sequences.
Input format FASTA
Computer skills Basic
Maintained No

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Publication for MethBLAST

MethBLAST citations

 (10)
call_split

Body Mass Index in Pregnancy Does Not Affect Peroxisome Proliferator activated Receptor Gamma Promoter Region (−359 to −260) Methylation in the Neonate

2016
PMCID: 4849114
PMID: 27144075
DOI: 10.4103/2141-9248.180272
call_split See protocol

[…] e primer sequences based on the in silico change of the gene sequence obtained from PubMed (NC_000003.11), and second, by obtaining theoretical products and running primer tests of specificity in the methBLAST sequence similarity search program.In the polymerase chain reaction (PCR) analysis the primers employed for PPARγ coactivator (PPARG) M3 were: 5’-aagacggtttggtcgatc-3’ (forward) and 5’-cgaaa […]

library_books

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy

2013
Genome Med
PMCID: 3978871
PMID: 24134860
DOI: 10.1186/gm500

[…] e Sequenom MassArray EpiTYPER (Sequenom, San Diego, USA), performed as previously described [,]. Amplicons were designed using the Sequenom EpiDesigner [] and MassArray [], and tested in silico using methBlast [] software. Oligonucleotide sequences were prepared (see Additional file : Table S1) such that forward primer sequences contain a 10 bp tag (AGGAAGAGAG) at their 5′ ends, and reverse primer […]

library_books

Different Involvement of Promoter Methylation in the Expression of Organic Cation/Carnitine Transporter 2 (OCTN2) in Cancer Cell Lines

2013
PLoS One
PMCID: 3797819
PMID: 24146874
DOI: 10.1371/journal.pone.0076474

[…] rried out. In , the genomic sequence of OCTN2 promoter was displayed and CpG sites were marked. One methylated sequence of OCTN2 spanning −325 to −92 bp in HepG2 cells was checked for alignment using MethBLAST and is presented in . Other methylated sequences from LS174T, QBC-939 and U251 cells are presented in Fig S1, S2 and S3. In , the methylation profiles showed that the rates of methylated CpG […]

library_books

HOXA4 Gene Promoter Hypermethylation as an Epigenetic Mechanism Mediating Resistance to Imatinib Mesylate in Chronic Myeloid Leukemia Patients

2012
Biomed Res Int
PMCID: 3591123
PMID: 23484077
DOI: 10.1155/2013/129715

[…] sulfite modified DNA (either methylated or not at its CpG dinucleotides) was used to confirm the amplification specificity of the designed primer. The primers were blast before synthesised, using the methBLAST software (http://medgen.ugent.be/methBLAST/). […]

library_books

Development of a multiplex methylation specific PCR as candidate triage test for women with an HPV positive cervical scrape

2012
BMC Cancer
PMCID: 3517769
PMID: 23176198
DOI: 10.1186/1471-2407-12-551

[…] version; 3) minimization of formation of intramolecular interactions within the primer (hairpins), dimerization with itself (self-dimers) or with primers for the other targets (cross-dimers) and 4) a methBLAST search at http://medgen.ugent.be/methBLAST/ to ensure target specificity of primers.Following primer redesign, the PCR efficiencies increased from 75% to 95% and 52% to 105% for CADM1 and MA […]

library_books

Aberrant DNA Methylation and Prostate Cancer

2011
Curr Genomics
PMCID: 3219844
PMID: 22547956
DOI: 10.2174/138920211797904061

[…] ion between methylated and unmethylated cytosine residues could be accomplished by designing the methylation-specific or bisulfite sequencing primers using software such as MethPrimer, MethMarker, or MethBLAST. MethPrimer detects CpG-specific parameters and islands and is essentially based on the primer3 algorithms for designing primers [,]. In addition, MethMarker used as epigenetic primer design […]


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MethBLAST institution(s)
Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Belgian EMBnet Node, Université libre de Bruxelles, Campus de la Plaine, Brussels, Belgium
MethBLAST funding source(s)
Supported by GOA-grant 12051203, FWO-grant G.0185.04, G.1.5.243.05 and G.0106.05, and a research grant from the Childhood Cancer Fund 'Kinderkankerfonds'.

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