User: Mehmet

gravatar for Mehmet
Mehmet660
Reputation:
660
Status:
Trusted
Location:
Japan
Last seen:
2 days, 22 hours ago
Joined:
5 years, 12 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 364 results • page 1 of 37 • next >
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Comment: C: Ortholog Protein Finding Tool
... you can use orthofinder, which is easy to run and produces many useful comparative genomics results as well as phylogenetic trees inculuding species tree and ortholog trees. [here is the link ][1] [1]: https://github.com/davidemms/OrthoFinder ...
written 20 days ago by Mehmet660
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Comment: C: Question about codeml
... For distribution along branches, it is better to use a concatenated file (all genes in a file) with a phylogenetic tree. If you want to comparisons between 2 species, you can perform pair-wise comparison; using sequence of two species without a phylogenetic tree. ...
written 5 weeks ago by Mehmet660
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Comment: C: Question about codeml
... it totally depends on you aim. For instance, If you see distribution of dN or dS values in scope of species, it is better to use a concatenated file that contains all genes and a phylogenetic tree. Doing so, you can see dN or dS values for each species overall. This reflects overall dN or dS distrib ...
written 5 weeks ago by Mehmet660
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Comment: C: Comparative Genome Analysis vs. Comparative Genomics
... A short description: https://en.wikipedia.org/wiki/Conserved_sequence ## several papers describing/using tools for indel detection. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S2 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-S11-S7 ...
written 7 weeks ago by Mehmet660
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Comment: C: Comparative Genome Analysis vs. Comparative Genomics
... First of all this is a very general question or approach. It is a huge area. you can compare many part of genomes. briefly, the two statements intend to find similar/dissimilar part of genomes. For instance, you can compare; 1. genome structures: coding/non-coding part, length, same elements, size ...
written 7 weeks ago by Mehmet660
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Comment: C: Should I do P-value adjustment in this case?
... You can report your results as: 1. Raw p-values 2. FDR correction at 0.05 3. FDR correction at 0.10 ...
written 8 weeks ago by Mehmet660
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Comment: C: RNASeq, gtf file
... [https://www.biostars.org/p/453264/#454147][1] [1]: https://www.biostars.org/p/453264/#454147 ...
written 4 months ago by Mehmet660
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Comment: C: Freebayes error message
... how many memory did you use? Mostly, core dumped error points lack of enough memory. Another possible reason for this error could be interrupted files. you may try to increase memory and check your bam files. ...
written 4 months ago by Mehmet660
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Comment: C: GO for novel species
... Have you checked Blast2GO for GO analysis? You can give DNA or protein sequences of your novel species as input to Blast2GO. Blast2Go uses multiple sources (interpro, PFAM etc) and map to GO term also gives PFAM ids for PFAM domain and description. Using GO given by Blast2GO you can perform GO enric ...
written 5 months ago by Mehmet660
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Comment: C: filtered tab delinited file with awk
... I guess FPKM is the 13th column. if so, you can print transcripts that have FPKM values greater than 0.5 as below. cat yourfile | awk '{if($13>=0.5) print}' > output ...
written 5 months ago by Mehmet660

Latest awards to Mehmet

Popular Question 4 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 4 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 4 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 4 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 5 months ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Student 5 months ago, asked a question with at least 3 up-votes. For Heatmap based with FPKM values
Scholar 6 months ago, created an answer that has been accepted. For A: Eucaryotic gene predictor within eucaryote genome
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 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
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 9 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
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Popular Question 9 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 10 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Great Question 10 months ago, created a question with more than 5,000 views. For How to cluster genes in heatmap
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 Phylogeny based on multiple sequences
Popular Question 12 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 13 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 13 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 13 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 15 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Great Question 15 months ago, created a question with more than 5,000 views. For How to cluster genes in heatmap

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