Timeline for Finding proteins in DNA sequence
Current License: CC BY-SA 3.0
18 events
| when toggle format | what | by | license | comment | |
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| Jan 4, 2014 at 0:05 | answer | added | swbarnes2 | timeline score: 2 | |
| Feb 13, 2013 at 18:20 | answer | added | Alan Boyd | timeline score: 5 | |
| Feb 13, 2013 at 17:14 | comment | added | terdon |
You are only interested in the best result here since that will be the coding gene. You do NOT want exhaustive (E), that is only useful for highly divergent sequences, not when working on the same species. Try this: exonerate -m p2g dna-polyI.e-coli.fasta e-coli-K12.fasta it took about 2seconds on my laptop and the first result is what you want.
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| Feb 13, 2013 at 14:30 | comment | added | atmosx |
I am trying to create some results. After reading the manuals - it has an incredible amount of options - I used the following cli: exonerate -Q protein -T dna -E -m protein2genome:bestfit dna-polyI.e-coli.fasta e-coli-K12.fasta and I'm waiting for it to finish. My hardware is a macbook air i5 1.7 Ghz with SSD.
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| Feb 13, 2013 at 12:17 | comment | added | terdon | The DNA sequence you have is the entire genome of the bacterium. It contains a multitude of ORFs coding for all sorts of proteins. What you need to do is use BLAST, or much better, exonerate as described in my answer. Translating the entire genome and then trying to find a single protein is both incredibly inefficient and prone to errors as well as very hard. | |
| Feb 13, 2013 at 10:11 | history | edited | atmosx | CC BY-SA 3.0 |
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| Feb 13, 2013 at 1:14 | history | tweeted | twitter.com/#!/StackBiology/status/301499621715357696 | ||
| Feb 13, 2013 at 0:02 | history | edited | atmosx | CC BY-SA 3.0 |
added 870 characters in body
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| Feb 12, 2013 at 23:38 | comment | added | atmosx | Hello @bobthejoe, could you give me links and offer a quick hint about why are they better suited? | |
| Feb 12, 2013 at 22:18 | comment | added | bobthejoe | Aren't the RBS and Shine Delgarno sequences a much better search term? | |
| Feb 12, 2013 at 19:12 | vote | accept | atmosx | ||
| Feb 12, 2013 at 18:36 | answer | added | terdon | timeline score: 13 | |
| Feb 12, 2013 at 17:26 | comment | added | atmosx | To give a clear example, all my data comes from ncbi (BLAST). How come that I can not match it? I've tried out all 6 possible conformations of ORFs and still I can't "produce" a sequence that matches the DNA-Poly3! :-/ | |
| Feb 12, 2013 at 17:24 | comment | added | atmosx | Yes I should not (by any means) re-invent anything. I can use algorithms already in use. I know there are very sophisticated tools for the job. What I really want to know to begin with is how it works, then I can use ready algorithms. | |
| Feb 12, 2013 at 17:20 | comment | added | terdon | OK, but do you need a totaly new algorithm or can you use existing tools like BLAST? If this is a computer science course, you should implement the algorithms yourself (I guess), if it is a bioinformatics course you should not reinvent the wheel. There are many, very, very good, programs that do what you need already. Is it OK to integrate them into your web interface? | |
| Feb 12, 2013 at 17:19 | comment | added | atmosx | I should write the program and put up a web interface. | |
| Feb 12, 2013 at 17:07 | comment | added | terdon | Do you need to write a program that does this or will existing tools be OK? | |
| Feb 12, 2013 at 16:21 | history | asked | atmosx | CC BY-SA 3.0 |