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SNP Cutter specifications


Unique identifier OMICS_14880
Name SNP Cutter
Interface Web user interface
Restrictions to use None
Input data SNPs to be genotyped, a customizable list of restriction enzymes and other parameters for primer design.
Programming languages Perl
Computer skills Basic
Stability No
Maintained No


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Publication for SNP Cutter

SNP Cutter citations


A Toolkit for bulk PCR based marker design from next generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

BMC Genomics
PMCID: 3534495
PMID: 23157543
DOI: 10.1186/1471-2164-13-637

[…] of flanking PCR primer pairs for large numbers of targets.Web-based tools which have been reported for design of CAPS markers from small numbers of sequences include BlastDigester [], SNP2CAPS [] and SNP Cutter []. None of these tools readily scale to large volumes of NGS data. Bulk design of primer sets to SNPs or other genome targets can be performed using the Primer3 executable []. Although the […]


LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs

BMC Genet
PMCID: 2709117
PMID: 19500380
DOI: 10.1186/1471-2156-10-26

[…] sis. Without the actual data set itself, users are unable to perform LD analysis. However, many types of software exist which provide information for genotyping, e.g. the SNPlex genotyping system [], SNP cutter [], SNP-RFLPing [], and V-MitoSNP []. These programs do not include an LD function though. It is thus still difficult for researchers to narrow down the number of SNPs for performing SNP ge […]

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SNP Cutter institution(s)
National Laboratory of Medical Genetics of China, Central South University, Changsha, Hunan, China; Department of Psychiatry, University of Chicago, Chicago, IL, USA
SNP Cutter funding source(s)
This work was supported by a Young Investigator Grant from NARSAD (National Alliance for Research in Schizophrenia and Affective Disorders) and NIH R01 MH65560-01 and R01 MH59535 and by the Chinese State ‘863’ program (2002BA711A07-08, 2002BA711A07-03), ‘973’ program (2001CB510302, 2004CB518601) and National Natural Science Foundation of China (30070410, 30123006, 30371530 and 30340078).

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