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chevron_left Multiple nucleotide sequence alignment Differential expression detection Conventional primer design Experiment design FISH probe design Primer design chevron_right

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AlleleID specifications


Unique identifier OMICS_15902
Name AlleleID
Software type Application/Script
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Mac OS, Windows
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes


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  • person_outline Beacon Designer Team

AlleleID citations


iTRAQ based quantitative proteomic analysis reveals the lateral meristem developmental mechanism for branched spike development in tetraploid wheat (Triticum turgidum L.)

BMC Genomics
PMCID: 5879928
PMID: 29606089
DOI: 10.1186/s12864-018-4607-z

[…] hamburg, germany) with sybr premix ex taq (takara bio, inc.). the cdna was amplified using specific primers (additional file : table s1). primer pairs were designed for qrt-pcr using the local alleleid software (ver. 6.0; the expression levels of the corresponding genes are presented relative to corresponding control samples […]


Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs

Front Plant Sci
PMCID: 5859231
PMID: 29593755
DOI: 10.3389/fpls.2018.00283
call_split See protocol

[…] the seven senna species and were thus selected for subsequent hrm analysis. conserved regions flanking the variable sites were identified visually and hrm-suited potential primers were designed with alleleid (v.7.7, premier biosoft international, palo alto, ca, united states) using its sybr green design function. the target amplification was set between 100 and 250 bases and primer length […]


Development and validation of a duplex real time PCR assay for the diagnosis of equine piroplasmosis

PMCID: 5834856
PMID: 29499748
DOI: 10.1186/s13071-018-2751-6

[…] af261824, ay058899, dq250541, u97167 and u97168, were retrieved from genbank and aligned using bioedit 7.0.9 []. primers and a minor groove binder (mgb) hydrolysis probe were designed using the alleleid 7.72 software (premier biosoft, palo alto, ca, usa). the software parameters were set to avoid cross-homology with the equine genome and cross-hybridization interference with the adopted […]


Transcripts within rod photoreceptors of the Zebrafish retina

BMC Genomics
PMCID: 5806438
PMID: 29422031
DOI: 10.1186/s12864-018-4499-y

[…] on a nanodrop spectrophotometer, and cdna was synthesized using the superscript® kit (new england biotech) using random hexamer primers. gene-specific primers used for qpcr were designed using alleleid7/84 (premier biosoft), and are provided in table . amplification was carried out using a model 7900ht fast real-time pcr system and sybr-green pcrmaster mix (applied biosystems, inc.). […]


Detection of 16S rRNA and KPC Genes from Complex Matrix Utilizing a Molecular Inversion Probe Assay for Next Generation Sequencing

Sci Rep
PMCID: 5794912
PMID: 29391471
DOI: 10.1038/s41598-018-19501-z

[…] removed and dna was extracted as described above according to manufacturer’s protocols., mip complementary 16s probe arms were designed utilizing clc genomic workbench (clc bio, cambridge, ma) and alleleid 7.73 (premier biosoft, palo alto, ca). primers were designed targeting the conserved regions flanking variable regions 1, 2, 3, 6 and 7 of the 16s based on their ability to distinguish […]


Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA

PMCID: 5908672
PMID: 29443017
DOI: 10.3791/55451

[…] flanking the its1 or its2 sequences: align the conserved regions from various species by clustalw. design primers specific for its flanking region after taxa specific/cross-species analysis with alleleid software. the two primer pairs amplifying ssu-5.8s and 5.8s-lsu amplicons can be designed based on the flanking regions of its1 and its2, respectively. because these amplicons are spanning […]

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