215 reputation
17
bio website convalesco.org
location Brno, Czech Republic
age 32
visits member for 1 year, 7 months
seen Jul 17 at 9:05

Pharmacy student, Apple addict, open source lover, ruby programmer, snowboarder.


Jul
14
comment To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)
@JackAidley Whether if needed it could express a particular protein (at any quantity).
Jul
14
comment To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)
I'm on to something using blast (I dropped out the idea of writing my own script to do this as soon as I played around with BLAST). I know that E. Coli can produce my protein (it's documented) at protein level. I couldn't find a perfect match thought, I've found a 74% positive match. Then searched about Desulfovibrio and found a 75% positive match (for a specific strain). I think it's enough, I can't take the risk to answer the question in a definitive way but, it's enough data to give some food for thought and possible direction. Comments are more than welcomed! Ty!
Jul
14
comment To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)
@DevashishDas No, I already have a gem with a list of fuzzy matching algorithms. I'd like to know if there's any other approach worth pursuing except that. NOTE: Any comment on the algorithms would be good also: Hamming, Jaro, JaroWinkler, Levenshtein, LongestSubsequence, LongestSubstring, PairDistance, Sellers. These are the ones supported by the library I'm going to use.
Jul
14
comment To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)
Of course @Chris, I will mention to my paper that it's possible to achieve the wanted result with cloning. Without your comment I wouldn't had that extra paragraph, which will make my paper better anyway :-) ... So thank you again!
Jul
14
comment To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)
Hello Chris. I'm not interested in to cloning anything but thanks for the info.
Feb
18
comment I'm 20. Can I still grow taller?
There's no normal way of getting 5cm at the age of 20. I'd say that you're more than fine, with 1.75 cm. The best thing to do is work on your posture.
Feb
16
comment Is it possible to give a person an allergic reaction in a very specific place?
You say "do the following", but there's no "following" sentence, so I don't know what you mean by "do the following". :-) - The hs reaction usually is "linear" but might have more than one variables, so I'd say that it's kind of dangerous to try it out on your own... Better visit a physician.
Feb
14
comment Is it possible to give a person an allergic reaction in a very specific place?
Well, yeah I was referring to allergies about trees, grasses, dust, etc. But sure, allergies are not 100% understood anyway.
Feb
13
comment Finding proteins in DNA sequence
Good!! Thank you Alan.
Feb
13
comment Finding proteins in DNA sequence
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.
Feb
13
comment Finding proteins in DNA sequence
@terdon I modified my initial question and added some more specific questions! Thanks for your help, it's very very much! You saved me quite some time!
Feb
12
comment Finding proteins in DNA sequence
Hello @bobthejoe, could you give me links and offer a quick hint about why are they better suited?
Feb
12
comment Finding proteins in DNA sequence
Sure, already did! Thanks again for the tips!
Feb
12
comment Finding proteins in DNA sequence
Hello, thanks for the explanation it was enlightening, I will try work on it tonight. Do you know which is the main procedure by which the protein is aligned to the DNA? :-) Thanks again!
Feb
12
comment Finding proteins in DNA sequence
Thanks for the answer! I will study the answer in a couple of hours when I'll have time! Thanks for your time!
Feb
12
comment Finding proteins in DNA sequence
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
comment Finding proteins in DNA sequence
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
comment Finding proteins in DNA sequence
I should write the program and put up a web interface.