User: Mehmet

gravatar for Mehmet
Mehmet540
Reputation:
540
Status:
Trusted
Location:
Japan
Last seen:
11 hours ago
Joined:
5 years, 5 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 346 results • page 1 of 35 • next >
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Answer: A: Eucaryotic gene predictor within eucaryote genome
... For gene prediction: Augustus can be used for initial gene prediction and results can be checked at Artemis and manually curated genes can be obtained. Later, those genes can be used as reference set and the initial gene prediction results can be compared by Eval tool to get gene prediction statist ...
written 2 days ago by Mehmet540
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Comment: C: detection positive selection using multiple copy genes in orthologs
... Sequence names are duplicated because the sequence names must match with the names in the tree. For instance; in the sequence file; names are : SpeciesA SpeciesA SpeciesA SpeciesB SpeciesB This is the name order in the tree as well. (SpeciesA, SpeciesB so on). When I use sequence name as differ ...
written 6 weeks ago by Mehmet540
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detection positive selection using multiple copy genes in orthologs
... Dear all, I have done positive selection analysis using one-to-one copy ortholog groups via codeml tool. But I have seen some papers in which multiple copy gene ortholog families were also used to test positive selection. When I tried to do same analysis (multiple copy approach), ETE tool used only ...
genome gene sequence written 6 weeks ago by Mehmet540 • updated 6 weeks ago by h.mon30k
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Comment: C: how to use tblastn
... First you need to make a database using `makeblastdb` command Second, you can search your query against the database using `tblastn` ...
written 3 months ago by Mehmet540
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Comment: C: Orthofinder:How to obtain single copy homologous sequences from result files
... You need something like this? https://www.biostars.org/p/274269/ ...
written 3 months ago by Mehmet540
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Comment: C: The best k mer to use for illumina data
... you can use this tool to see K-mer distribution in your data. [jellyfish][1] [1]: https://www.cbcb.umd.edu/software/jellyfish/ ...
written 3 months ago by Mehmet540
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Comment: C: Orthofinder:How to obtain single copy homologous sequences from result files
... Can you define your question with more details? What do you want to do? In OrthologsIDS.txt file there are ortholog families with one gene in each ortholog family from each species. ...
written 3 months ago by Mehmet540
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Comment: C: UpsetR intersection numbers
... OK.I have solved and I am explaining here. UpsetR requires a binary data frame (numbers with zero and one only). Numbers bigger than 1 should replace with 1.The, `upset` function reads the data frame and produces graphs after calculating intersection size. Probably, UpsetR ignores if a row is not ...
written 3 months ago by Mehmet540
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Answer: A: UpsetR intersection numbers
... I converted mydata to a list as below: > str(mydata) List of 7 $ A: int [1:99] 0 0 0 0 0 0 0 0 0 1 ... $ B: int [1:99] 2 0 0 0 0 0 0 0 0 1 ... $ C: int [1:99] 1 0 0 0 0 0 0 0 0 1 ... $ D: int [1:99] 9 5 5 14 5 7 10 11 0 6 ... $ E: int [1:99] 1 0 0 0 0 0 0 0 0 1 . ...
written 3 months ago by Mehmet540
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Comment: C: UpsetR intersection numbers
... Thank you for reply, but it did not change. I selected F and G columns only to test using two different functions below: in the first code I used `upset` function only and in the second code I used `fromList` function as well. But results are different. I attached two figures (fromList and upset t ...
written 3 months ago by Mehmet540

Latest awards to Mehmet

Scholar 2 days ago, created an answer that has been accepted. For A: Eucaryotic gene predictor within eucaryote genome
Popular Question 13 days ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 28 days ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 9 weeks ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Voter 11 weeks ago, voted more than 100 times.
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 3 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Great Question 3 months ago, created a question with more than 5,000 views. For How to cluster genes in heatmap
Popular Question 5 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 5 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 5 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 6 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 7 months ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 7 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Great Question 8 months ago, created a question with more than 5,000 views. For How to cluster genes in heatmap
Popular Question 8 months ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 8 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 8 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Great Question 9 months ago, created a question with more than 5,000 views. For Heatmap based with FPKM values
Popular Question 11 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 11 months ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 11 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences

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