User: psschlogl

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psschlogl30
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Posts by psschlogl

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Data randomization for apply some statistics
... Comments were add to the initial question ...
written 5 days ago by psschlogl30
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Comment: C: Data randomization for apply some statistics
... Hi JC I thinking in Bonferroni correction, two-sided Fisher’s exact test for kmers, at least for the moment, but I am checking other possibilities. Thanks ...
written 5 days ago by psschlogl30
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Comment: C: Data randomization for apply some statistics
... None? 8( >>>>>>>>>>>>>>>>>>>> ...
written 5 days ago by psschlogl30
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Data randomization for apply some statistics
... Hi there I have a quick question. I am dealing with some gigabits of fasta files and I am trying to develop a statistical analysis of protein composition (count aacs, kmers and using some probabilistic models) and I need some random data to use. I have the done the code to randomization and my que ...
fasta sequence proteins written 5 days ago by psschlogl30
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Comment: C: Trying to use CD-HIT with a fasta file with 5 mers but not getting any output.
... Thank you gb. I will check out your suggestions to understand the theory with blast. Thanks for your time and patience. I am very grateful for all you guys have doing for my learning! ...
written 20 days ago by psschlogl30
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Comment: C: Trying to use CD-HIT with a fasta file with 5 mers but not getting any output.
... I think i give it a much bigger file ;) ...
written 20 days ago by psschlogl30
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Comment: C: Trying to use CD-HIT with a fasta file with 5 mers but not getting any output.
... I will try to use a different file. Now I got it with cd-hit. cd-hit -i kmers_cdHit_test.faa -c 0.8 -o cdhitout -n 5 -l 4 ================================================================ Program: CD-HIT, V4.8.1, Mar 01 2019, 14:14:47 Command: cd-hit -i kmers_cdHit_test.faa -c 0.8 - ...
written 20 days ago by psschlogl30
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Comment: C: Trying to use CD-HIT with a fasta file with 5 mers but not getting any output.
... It is in my first question. I think i tried -c 0.8 but not -n2. I will check gb. Thank you cd-hit -i pentamers -c 0.8 -o cdhitout -n 2 -l 2 ================================================================ Program: CD-HIT, V4.8.1, Mar 01 2019, 14:14:47 Command: cd-hit -i pentamers ...
written 20 days ago by psschlogl30
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Comment: C: Trying to use CD-HIT with a fasta file with 5 mers but not getting any output.
... Hi Joe my intentions are to cluster all motifs (20**5) in groups of shared/similar aac compostions, i.e. those that are permutations of a single sequence. there would have different groups of kmers like: a1b1c1d1e1 , a1b1c1d2 , a1b2c2 .... a5 . Each cluster would have to include compositions as a ...
written 20 days ago by psschlogl30
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Comment: C: Trying to use CD-HIT with a fasta file with 5 mers but not getting any output.
... Hi Joe I have done something like this: alphabet = 'ACDEFGHIKLMNPQRSTVWY' def get_all_possible_kmers(alphabet, k): """Returns a list of all possible combinations of kmers of length k from a input alphabet.""" return (''.join(x) for x in itertools.product(alphabet, repe ...
written 21 days ago by psschlogl30

Latest awards to psschlogl

Supporter 27 days ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Trying to run clustalw with biopython on jupyter notebook
Scholar 9 months ago, created an answer that has been accepted. For A: Trying to run clustalw with biopython on jupyter notebook

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