AlleleID protocols

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AlleleID specifications


Unique identifier OMICS_15902
Name AlleleID
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes



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AlleleID in pipelines

PMCID: 5859231
PMID: 29593755
DOI: 10.3389/fpls.2018.00283

[…] 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 […]

PMCID: 5300195
PMID: 28182701
DOI: 10.1371/journal.pone.0171483

[…] cdna was synthesized from 900 ng of total rna using primescript rt reagent kit (takara, dalian, china) according to the manufacturer's instruction. the cdna specific primers were designed using alleleid 6.0 software (). 28s ribosomal protein s5 (rps5), elongation factor 1 alpha (ef1α) and elongation factor 1 beta (ef1β) were chosen as the housekeeping genes for ss, sa and aa respectively. […]

PMCID: 3589332
PMID: 23472178
DOI: 10.1371/journal.pone.0058316

[…] species, sequence data obtained from genbank were aligned using bioedit and a number of sets of putatively species-specific pcr markers were designed in silico using the computer software package alleleid (premier biosoft, inc.) or the primer-blast function in genbank (, candidate primer sets were screened for positive amplification […]

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AlleleID in publications

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 […]

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 […]

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.). […]

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 […]

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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