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Amplicon is a Python script for designing PCR primer sets. Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
software for analyzing and visualization of the results of deep amplicon sequencing cite: STUGLIK, M. T., RADWAN, J. and BABIK, W. (2011), jMHC: software assistant for multilocus genotyping of gene families using next-generation amplicon sequencing. Molecular Ecology Resources, 11: no. doi: 10.1111/j.1755-0998.2011.02997.x http://doi.wiley.com/10.1111/j.1755-0998.2011.02997.x
AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal.
This project is useful for targeted sequencing and capture probe creation on a genome scale. It runs as a single command-line script. Options are given below: % ./pckme.py --helpUsage: pckme.py [options]Options: -h, --help show this help message and exit --email=EMAIL users email address to send the data files --obed=OBED output file name --ozip=OZIP output file name -f FILENAME, --file=FILENAME the input file for primer design required as a fullpath could should be 2 column (chr and position) o
CANGS DB is a user-friendly and stand-alone database tool for processing, analyzing and managing the high throughput sequencing data from 454 amplicon resequencing projects. CANGSDB is very easy to use; it could be installed and used on any UNIX based computer to handle individual as well as multiple sequencing projects. It provides full-fledged flexibility with various options in raw sequence processing and analysis. CANGS DB provides a very powerful data retrieval interface, which enables rese
Important: We plan to update MPprimer and make it more useful, anyone who has any ideas please contact me. Thanks. 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 conside