User: pltbiotech_tkarthi

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Posts by pltbiotech_tkarthi

<prev • 62 results • page 1 of 7 • next >
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Answer: A: Why some CDS is enlisted as non translating CDS at ENSEMBL (Plant) when it is ac
... Thanks Lieven Sterck for your kind reply. It's true one of the transcript that I am interested is not translated to a protein, it could be a pseudogene, thanks again for your suggestions. ...
written 19 days ago by pltbiotech_tkarthi170
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Why some CDS is enlisted as non translating CDS at ENSEMBL (Plant) when it is actually encoding for a protein?
... I am interested in a CDS at ENSEMBL, but I found it is Nontranslating CDS and not encoding for a protein. But for the same nucleotide sequence, putative protein is reported in NCBI based on computational annotation and translation. I would like to know, why in ENSEMBL it is enlisted as non translati ...
gene sequence written 23 days ago by pltbiotech_tkarthi170
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Comment: C: evolution of gene
... All the best @Learner, through your question I am also learning, thanks for your question about the concept of new gene evolution! ...
written 12 weeks ago by pltbiotech_tkarthi170
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Comment: C: evolution of gene
... I agree @jrj.healey, the evolution of a gene happened is an unanswerable question, but there must be a natural selection process in which the ancestral unstructured gene should have acquainted with mutations and structuration for the origin of new gene with further fixation of favorable alleles in a ...
written 12 weeks ago by pltbiotech_tkarthi170
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Comment: C: Number of species for positive selection analysis
... Hi rprog008, Nobody is trying to prove your answer is wrong? but you said "I know you will come up will new idea of blame game". Do I repeat this same question and statements to you. Of course without any man made procedure and human brain input, how the computer will do the analysis itself. " Ev ...
written 12 weeks ago by pltbiotech_tkarthi170
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Comment: C: Number of species for positive selection analysis
... The Research Gate conversation was about number of sequences, you can go through that Research Gate conversation again, even someone tends provide the information about the use of even 4 species at smaller scale analysis, however the same person suggested to use more than 10 sequences, which means o ...
written 12 weeks ago by pltbiotech_tkarthi170
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Comment: C: Number of species for positive selection analysis
... I know that one should use large data set than smaller ones. My question is not that, how you can claim that one should not use less than 10 species as you have written here? Even you can see above from the statements of sammy.ich17 stated "For instance some papers used single copy ortholog alignme ...
written 12 weeks ago by pltbiotech_tkarthi170
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How to extract genomic positions of SNPs using snp-sites?
... By using snp-sites (https://github.com/sanger-pathogens/snp-sites) I extracted the SNPs with Linux command: snp-sites file name.fasta. This script just extracting the SNPs without position information. I know the genomic positions of my reference sequence. My question is: How to add the genomic posi ...
genome alignment snp sequencing written 12 weeks ago by pltbiotech_tkarthi170
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Comment: A: Number of species for positive selection analysis
... Hello rprog008, Do you have reference that suggest one should not use less than 10 species for Maximum Likelihood method? ...
written 12 weeks ago by pltbiotech_tkarthi170
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Answer: A: Help with mRNA region annotation
... You have answer from your statements itself as you mentioned the CDS:172-1443, then beyond these limits you should have UTRs at 5' and 3' ends of your mRNA as you have also given the UTRs positions. If you wish to confirm, you should also have genomic sequence to align your mRNA using tools like spl ...
written 12 weeks ago by pltbiotech_tkarthi170

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Scholar 7 months ago, created an answer that has been accepted. For A: mean Tajima's D value

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