User: Cytosine

gravatar for Cytosine
Cytosine440
Reputation:
440
Status:
Trusted
Location:
Ljubljana, Slovenia
Last seen:
1 year, 6 months ago
Joined:
4 years, 11 months ago
Email:
v*************@gmail.com

Posts by Cytosine

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Maximum Likelihood Inference
... Did you give a try to [RAxML][1] already? [1]: https://sco.h-its.org/exelixis/web/software/raxml/index.html ...
written 2.1 years ago by Cytosine440
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Comment: C: Network proxy error during "myRast" commands
... Hard to guess then... First thing I would do is check whether the server is accessible at all. Can you manually ping/telnet the server from your terminal? If no, then you need to configure the system, if yes then you need to modify the script. I'm not familiar with MyRast so I can't give you any ...
written 3.4 years ago by Cytosine440
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Comment: C: Genotype notations for complete genomics data
... Never seen anything like this before, sorry. Maybe similar to https://www.biostars.org/p/166758/? ...
written 3.4 years ago by Cytosine440
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Comment: C: Bioinformatics Perl Help
... Perhaps you should try preparing a script to do this task for a file with just 1 sequence. After you prepare the correct output for this 1 sequence, expand the script to do this task in a loop for more sequences. ...
written 3.4 years ago by Cytosine440
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Comment: C: Network proxy error during "myRast" commands
... Maybe try setting your proxy environment variable in the terminal session? Or try the LWP::UserAgent module inside the script for setting the proxy. Suggested from: http://stackoverflow.com/questions/1746614/use-proxy-with-perl-script ...
written 3.4 years ago by Cytosine440
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Comment: C: hmm - Format of the observation sequence required for the ViterbiCalculator
... If you have the transition and emission probability matrices available, then you can test the HMM on a smaller set and precompute the optimal path by hand. That should show you if the hidden states you calculated are the same ones as proposed by the HMM on the smaller set. Whether or not your pred ...
written 3.4 years ago by Cytosine440
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Comment: C: hmm - Format of the observation sequence required for the ViterbiCalculator
... How did you derive your transmission and emission probabilities? Did you train the HMM on a training set?   ...
written 3.5 years ago by Cytosine440
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Comment: C: Which mitochondrial genomes in RefSeq are complete?
... Thank you, but I'm already using that one, which is a RefSeq subset of mitochondrial genomes. However, it also contains the same entries which are in the WGS section and made me post the original question. ...
written 3.7 years ago by Cytosine440
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Comment: C: How to get identical sequences from multiple sequence alignment
... How about making another alignment of the FASTA file, from which you deleted the unwanted sequence? ...
written 3.7 years ago by Cytosine440
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Which mitochondrial genomes in RefSeq are complete?
... This one has me puzzled... I'm trying to compare mitochondrial genomes and I'm looking for the complete and finalized versions from genbank only. So far, I've thought that the RefSeq database would be the place to look in, but I've stumbled across 2 entries that got me thinking. (both of them are ...
ncbi genome refseq genbank written 3.7 years ago by Cytosine440 • updated 3.7 years ago by Jeremy Leipzig18k

Latest awards to Cytosine

Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Extract common differentially expressed genes (DEGs) of different data sets. (Mi
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Most suitable alignment program for Ka/Ks analysis of whole genome coding sequences
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Proper normalization method
Supporter 4.8 years ago, voted at least 25 times.
Good Answer 4.9 years ago, created an answer that was upvoted at least 5 times. For A: Which programming language to integrate several open source software into one wo
Scholar 5.0 years ago, created an answer that has been accepted. For A: Extract common differentially expressed genes (DEGs) of different data sets. (Mi
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Extract common differentially expressed genes (DEGs) of different data sets. (Mi
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Extract common differentially expressed genes (DEGs) of different data sets. (Mi
Scholar 5.0 years ago, created an answer that has been accepted. For A: Extract common differentially expressed genes (DEGs) of different data sets. (Mi

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