This repository contains code for finding discriminatory primers among genomes of interest. Please refer to the following: CITATION (method and application to human bacterial pathogens, sub-serotype resolution): Pritchard L, Holden NJ, Bielaszewska M, Karch H, Toth IK (2012) "Alignment-Free Design of Highly Discriminatory Diagnostic Primer Sets for Escherichia coli O104:H4 Outbreak Strains." PLoS ONE 7(4): e34498. doi:10.1371/journal.pone.0034498 CITATION LINK: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034498 or CITATION (application to plant pathogens, species-level resolution) Pritchard L, Humphris S, Saddler GS, Parkinson NM, Bertrand V, Elphinstone JG, Toth IK (2013) "Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences." Plant Pathology, 62, 587-596 doi:10.1111/j.1365-3059.2012.02678.x CITATION LINK http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3059.2012.02678.x/full DEPENDENCIES: Any of the following Dependencies can be used for running the 'find_differential_primers.py' pipeline: >> biopython : v1.57 - v1.61 Git Hub version : https://github.com/biopython/biopython Older Releases (scroll to bottom): http://biopython.org/wiki/Download >> bx-python : current Hg (Mercurial) version works as of June 19, 2013 Hg version : https://bitbucket.org/james_taylor/bx-python/src >> EMBOSS (for eprimer3) : v6.30, v6.31, v6.4.0 http://emboss.sourceforge.net/download/ >> primer3 : v1.1.4 http://primer3.sourceforge.net/releases.php >> prodigal : v1.20 http://code.google.com/p/prodigal/downloads/list?can=1&q=&colspec=Filename+Summary+Uploaded+ReleaseDate+Size+DownloadCount >> BLAST / BLAST+ : v2.2.22 / v2.2.22+ (Other versions may work) http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download BASIC USE: If you do not have complete genome sequences use the 'stitch_six_frame_stops.py' script to stitch together the contigs of a single genome (contained within one multi-FASTA formatted file). The script does this by stitching the contigs with the following sequence 'NNNNNCATTCCATTCATTAATTAATTAATGAATGAATGNNNNN'. This sequence contains start and stop codons in all frames. Remember the default workflow is to only find primers within CDS regions. Once all genomes have been stitched together, make a config file similar to the example within the 'O104_primers_5.conf' file. Finally, run 'find_differential_primers.py'. FURTHER INFORMATION: Read the comments contained within the top of each '*.py' file as well as the Supporting Information ('Methods S1' document) of the above CITATION. CONTRIBUTORS ============ Leighton Pritchard https://github.com/widdowquinn Benjamin Leopold https://github.com/cometsong Michael Robeson https://github.com/mikerobeson
cometsong/find_differential_primers
Scripts to aid the design of differential primers for diagnostic PCR.
Python