Does anyone know any good in silico PCR algorithm, preferably for offline use. Input would be a multifasta file and forward and reverse primer sequences. Output would preferably be substrings with intact headers.
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How about the tool by Jim Kent that's used by UCSC?
In-Silico PCR was written by Jim Kent. Interactive use on this web server is free to all. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available. Contact Jim for details.
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There's an hgPcr in the lastest copy of jksrc.zip. I've yet to to look into the code yet to determine if it's the same as the hgPcr in silico PCR on the website.
Edit: Or you can go to
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Originally posted by winsettz View PostThere's an hgPcr in the lastest copy of jksrc.zip. I've yet to to look into the code yet to determine if it's the same as the hgPcr in silico PCR on the website.
Edit: Or you can go to
http://genome-source.cse.ucsc.edu/gi...91e433;hb=HEADsavetherhino.org
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mothur has a function called pcr.seqs that supposedly does what you're looking for. http://www.mothur.org/wiki/Pcr.seqs
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Originally posted by rhinoceros View PostYeah, thanks. I was just going through the zip file. Problem is though that it has a bunch of dependencies and among other things requires a running mysql server. This is all a bit extensive for wanting to do just one relatively simple thing..
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Originally posted by mcnelson.phd View Postmothur has a function called pcr.seqs that supposedly does what you're looking for. http://www.mothur.org/wiki/Pcr.seqssavetherhino.org
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You can also try ipcress
Cheers,
Scott.
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Originally posted by id0 View PostThat was my experience as well. I ended up building a scraper for the UCSC PCR page. It took a few seconds per lookup, so doing hundreds of searches took a while, but not an unreasonable amount of time. Unfortunately, if you try to perform multiple queries from the same IP concurrently, the IP is automatically blocked for a day, so there is no way to parallelize that.
The provided macIntel binaries (faToTwoBit, gfServer, gfPcr) work almost out of box on recent Mac OS X. I only needed to symlink /opt/X11/lib/libpng14.14.dylib to /usr/local/libsavetherhino.org
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So, I ended up using pcr_seq from biopieces. The below code yields the results I was expecting:
Code:read_fasta -i input.fasta | pcr_seq -f CCTACGGGRSGCAGCAG[1,0,0] -R ACCGCGGCKGCTGGC[1,0,0] | grab -e 'REC_TYPE eq PCR' | write_fasta -x > PCR_products.fasta
On related note, I hadn't used biopieces before. I have to say, I'm positively surprised. There seems to be a ton of very useful scripts included. E.g. plot_lendist appears to be a very easy (little work) way to plot length distribution with high quality output, i.e. to check the output of previous code (except on bacterial subset of Silva SSURef_NR99_115):
Code:read_fasta -i PCR_products.fasta | plot_lendist -xk SEQ_LEN -t post -o plot.ps -L
..works pretty wellLast edited by rhinoceros; 10-27-2013, 04:41 AM.savetherhino.org
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