Search Results for "pcr"
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Showing 36 open source projects for "pcr"
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Gemi
PCR primers / probes design from multiple & degenerate sequences
Gemi can be downloaded from the site (https://sites.google.com/site/haithamsobhy/software). Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional... -
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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FullSSR
SSR detection and primer designing software
Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step. -
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OligoYap Portable
Oligo design and bioinformatic analysis software.
OligoYap can be used to design classical PCR, SYBR Green, TaqMan, MGB, Molecular Beacons, Microarray and Real-Time PCR primers/probes and for bioinformatics analysis. It has the features of enzyme cut analysis, mutation analysis, DNA/protein match and BLAST. You can easily record laboratory materials/files, prepare PCR mix and many other laboratory operations. It works on windows8.1 and earlier operating systems, but has not been tried on windows10 and later. For better images, you can right... -
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miRprimer
Automatic design of primers for miR-specific RT-qPCR
miRprimer designs primers for PCR amplification of microRNAs as described (Busk (2014). A tool for design of primers for microRNA-specific quantitative RT-qPCR. BMC Bioinformatics. 15, 29) for use with the method miR-specific RT-qPCR (Cirera, S., and Busk, P.K. (2014). Quantification of miRNAs by a simple and specific qPCR method. Methods in Molecular Biology. 1182, 73-81.). The program was written in Ruby and is available as source code for developers and as an .exe file for easy use. -
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WellMeth
Genome-Wide DNA Methylation Analysis with RRBS
WellMeth is a integrated framework for Reduced Representation Bisulfite-Seq analysis -
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DEBay
Deconvolutes qPCR data to estimate cell-type-specific gene expression
DEBay: Deconvolution of Ensemble through Bayes-approach DEBay estimates cell type-specific gene expression by deconvolution of quantitative PCR data of a mixed population. It will be useful in experiments where the segregation of different cell types in a sample is arduous, but the proportion of different cell types in the sample can be measured. DEBay uses the population distribution data and the qPCR data to calculate the relative expression of the target gene in different cell types... -
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RDML stands for Real-time PCR Data Markup Language and is the standard file format for export, storage and exchange of quantitative PCR (qPCR) data. This project focuses on the development, implementation and enhancement of the RDML file format and its description (XML schema).
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PrimerSeq
Designs primers on flanking constitutive exons for RT-PCR
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MPprimer
a program for reliable multiplex PCR primer design
Background: Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer... -
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Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
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pyQPCR is a GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu
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Lab Studies
Rediscover the Simplicity http://www.atgclabs.com/
... and analytical phenotypic assays are used. Animal Studies application is web-based and completely customizable, with Animal Studies it is very simple to create, change and distribute data flows using an iterative approach. Animal Studies puts all the information right at your fingertips. The Animal Studies module provides storage for the genotype information, organise genotyping protocols and archive genetic marker information, including for example PCR conditions and results. -
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InMethyl
Design of target-specific primers for bis. sequencing of CpG-islands
InMethyl is a Python-based application for the design of target-specific primer combinations for PCR amplification and bisulfite sequencing of complete CpG-islands. InMethyl uses bowtie high-throughoutput aligner to identify potential mis-priming sites in the bisulfite treated or intact genome and then – undesirable potential PCR products. InMethyl provides a balance between various characteristics that allows to pick up primers in hard-to-study genomic regions. This balance is based... -
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CIMS
Crosslinking induced mutation site analysis
This package includes the scripts to detect statistically reproducible crosslinking induced mutation sites (CIMS) and cross linking induced truncation sites (CITS) from HITS-CLIP data. References: Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols, 9:263-293. Zhang,C.†, Darnell, R.B.† 2011.... -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
DEW is a platform that allows users to explore RNA-Seq data. A web-based Graphical User Interface is included. The analysis proceeds as such: gapped alignments are performed and corrected for length, PCR and fragment bias so that a Fragment Per (effective) Kilobase per Million of reads (FPKM) is estimated as well as the simpler Reads Per Kb per Million of reads (RPKM). When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization algorithm... -
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating... -
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HBSAnalyzer
Aligner and methylation caller for hairpin bisulfite sequencing data
HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence... -
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HBSAnalyzer
Aligner and methylation caller for hairpin bisulfite sequencing data
HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence... -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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mPSQed
Alignment editor and multiplex pyrosequencing assay designer
Molecular-based diagnostic assays are the gold standard for infectious diseases today, since they allow a rapid and sensitive identification and typing of various pathogens. While PCR can be designed to be specific for a certain pathogen, a subsequent sequence analysis is frequently required for confirmation or typing. The design of appropriate PCR-based assays is a complex task, especially when conserved discriminating polymorphisms are rare or if the number of types which need... -
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PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.
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This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. "Novel computational methods for increasing PCR primer design effectiveness in directed sequencing". BMC Bioinformatics 2008, 9:191.
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FAS-DPD is a program to design degenerate primers for PCR.