User: odoluca

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odoluca20
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20
Status:
New User
Location:
Turkey/Izmir/Izmir University of Economics
Website:
http://homes.ieu.edu.t...
Last seen:
11 months, 2 weeks ago
Joined:
1 year, 7 months ago
Email:
o***********@ieu.edu.tr

Posts by odoluca

<prev • 9 results • page 1 of 1 • next >
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Comment: C: match, mismatch, gap parameters for short DNA motifs
... I checked the CD-HIT. Its webservers don't allow any file bigger than 50 MBs. So I have to compile myself. However, I already coded a pairwise comparison algorithm, so I want to stick with it, in which otherwise would take longer. Thanks anyways. ...
written 12 months ago by odoluca20
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match, mismatch, gap parameters for short DNA motifs
... Hello all, I have millions of short DNA sequences (20-150 nt) and I suspect some of these show similarity. I would like to compare them using pairwise alignment method, however, I am having trouble in determining which match score, mismatch penalty and gap penalty (linear method) I should use. My r ...
motif pairwise alignment dna written 12 months ago by odoluca20
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Answer: A: Good Source For Dna Substitution Score Matrix / Matrices?
... Hello TabeaH, I was wondering if you managed to find any substitution matrix catalog. I have short non-coding DNA motifs to be aligned and I am not sure which substiution matrix and gap penalties I should use. Any idea? Cheers ...
written 12 months ago by odoluca20
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multilabel clustering/classification based on sequence silimarity
... I have been dealing with a new issue regarding clustering/classifying sequences. I need an algorithm that can cluster huge number of short sequences. To simulate the problem I have made some visuals and a small set of sequences. ![fig1][1] http://uploads.im/zxAZC.png From the image it should b ...
pairwise sequence classification clustering written 15 months ago by odoluca20 • updated 15 months ago by Biostar ♦♦ 20
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Comment: C: Help with building bioinformatics workstation
... About cloud computing-It is still a confusing subject for me. Such as How to set it up. Also predicting my requirements such as ram per processor can be so off-target.... ...
written 16 months ago by odoluca20
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Comment: C: Help with building bioinformatics workstation
... It turns out you were right. I was using an external python module but I rewrote the algorithm and used numba.jit to speed it up by ten fold. ...
written 16 months ago by odoluca20
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Comment: C: Help with building bioinformatics workstation
... I have ordered 8 kvr24e17d8/16 16 gb dimms and waiting. I ll ket you know how it turns out. ...
written 16 months ago by odoluca20
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simple statistics question
... Hello, I am trying to do some statistics and feel stuck under piles of statistical tests. Simply, I have a population of values with unknown mean or standard deviation. I pulled one value, let's say: 35, using method A. And I want to test if 35 is within %0.05 upper tail of the population distribut ...
statistics written 18 months ago by odoluca20 • updated 18 months ago by Alex Reynolds27k
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Help with building bioinformatics workstation
... My work focus on analysis of genomes (including human) to discover new motifs and clustering them. The clustering step alone takes a huge amount processing power. I estimate that clustering step, alone, will take approximately 2 **months** using my current computer (all 4 cores loaded, i5 4670K@4.1G ...
computer hardware ecc ram workstation written 19 months ago by odoluca20 • updated 18 months ago by LLTommy1.2k

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Popular Question 15 months ago, created a question with more than 1,000 views. For Help with building bioinformatics workstation

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