Search Results for "primer 5"
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Showing 18 open source projects for "primer 5"
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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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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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VIA attention Up
Videojuego para aumentar los niveles de atención
VIA es un juego con técnicas de Interfaz Cerebro Computador y de Neurofeedback, donde cualquier persona puede entrenar y mejorar sus niveles de atención después de repetidas sesiones. De esta manera será una herramienta útil para apoyar la labor de los psicólogos. El objetivo del juego se basa en un jugador que debe concentrarse lo suficiente para poder ganar una carrera de carros. El primer nivel del juego es de entrenamiento, en el cual aparecerán unas gasolinas de color azul por un... -
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Matchup
Bioinformatics tool for universal primers and group-specific probes
Matchup program can be used to find universal primers and group-specific probes for DNA-based detection methods llike AFLP(Amplification fragment length polymorphism) or Microarray experiment. -
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primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to...
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easyPAC
easy Primer prediction from Alignments and Consensus sequences
Primer prediction from alignments and consensus sequences. easyPAC applies all standard quality tests to degenerate primer and primer pairs and optionally maps all primer candidates to an arbitrary number of reference files like repeat databases or genomes to ensure target specifity. -
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multipsq
Analysis of pyrograms form multiplex pyrosequencing experiments
A software for the classification of organisms based on results from multiplex pyrosequencing algorithms performed on the Pyro-Mark ID System (Qiagen). The assays can be designed using the software mpsqed available from https://sourceforge.net/projects/mpsqed/ Pyrosequencing can be applied for Single-Nucleotide-Polymorphism (SNP)-based pathogen typing or for providing sequence information of short DNA stretches. However, for some pathogens molecular typing cannot be performed relying on a... -
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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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Store App
1.0
Store, es el Primer servicio de Caliburnus, que ofrece oportunidades a las Aplicaciones Gratuitas. De manera tal, que la gente conozca las alternativas a aplicaciones PAGAS. -
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BatchPD
BatchPD: Batch automation of a primer design pipeline for human genes
BatchPD is a primer design program developed to address the needs of clinical diagnostics laboratories to design primer oligos for PCR amplification against human gene exons, taking into account of SNPs where possible. Research paper publication: http://www.bioinformation.net/008/97320630008365.htm BatchPD checks specificity via in-silico PCR, provide gene/exon specific relevant information summarised in an end spread-sheet; Primer design, PCR checks and other relevant information are... -
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is... -
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Zimlet Task Panel
Zimlet adaptado para Tareas y Calendario
Panel de Tareas y Calendario para visualizar en primer plano el estado de las tareas y la situción a una semana vista del calendario. -
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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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RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying and determining relative frequency of candidate primers for Random Amplification of Polymorphic DNA (RAPD) assays.
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IMP is an automated tool for intron-flanking primer design based off of Expressed Sequence Tags (ESTs). It's intended for use in species with limited to no genomic sequence data available.
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ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences
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Autoprime
Automated primer design using EnsEMBL
AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression. By connecting to the EnsEMBL database gene structure information is used to find primers spanning exon borders. This way only expressed sequences are captured. Additionally mispriming on repetitive regions can be avoided using information from RepBase.
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