User: chahatupretiiitk

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3 years, 3 months ago
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Posts by chahatupretiiitk

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Finding restriction sites when the gene is on the negative strand
... Thanks Anima, this was quite helpful. I will let you know if I have any further questions! ...
written 14 hours ago by chahatupretiiitk50
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Comment: C: Finding restriction sites when the gene is on the negative strand
... Thanks @Wouter for the reply. What I am confused is if the restriction sites on the positive strand would map to the same locations on the -ve strand too. Believe me, I have drawn quite a few diagrams since yesterday :) ...
written 1 day ago by chahatupretiiitk50
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Finding restriction sites when the gene is on the negative strand
... Hi, This might be a naive question, but it has been troubling me for a bit. I have the human genome (hg19) cut by 2 restriction enzymes and I have a list of cut sites. I am assuming that this is by default the +ve strand of the DNA. Now I have a gene whose location is `chr11 355953 357144 -` meani ...
rna strand dna written 1 day ago by chahatupretiiitk50 • updated 1 day ago by Anima Mundi2.3k
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Comment: C: how to find the total number of recognition sequence of a restriction enzyme in
... Hi Erik, Thanks a lot for this nice tool! I had a question related to this. I want to find cut sites in a human genome for 2 restriction enzymes whose names I do not know (they are not disclosed by the company), but I do know their cut sites, which are GATC^ and GANT^C (here N stands for any nucleo ...
written 5 days ago by chahatupretiiitk50
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Comment: C: Genomic Restriction Finder
... Hi Pierre, Thanks a lot for this awesome tool. I am not sure if commenting on this old thread is good, but I had a quick question about the tool. I wanted to cut hg18 using 2 enzymes whose name I do not know (it's provided by a company) but I do know that the restriction sites for the 2 are - GATC^, ...
written 6 days ago by chahatupretiiitk50
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Comment: C: Is there gold standard data for ancestral reconstruction?
... Got it, thanks a lot! ...
written 21 days ago by chahatupretiiitk50
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Comment: C: Is there gold standard data for ancestral reconstruction?
... Thanks Jean-Karim, the second paper was exactly what I was looking for. BTW, why do you think that using simulation is a better idea? ...
written 22 days ago by chahatupretiiitk50
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Comment: C: Is there a gold standard for ancestral reconstruction?
... In the papers for these tools, they do not report any dataset, just the fact that they provide these services. The papers of MrBayes has only the mathematical model used, the papers for MEGA provide performances but not for ancestral reconstruction, and I was unable to find the corresponding paper f ...
written 4 weeks ago by chahatupretiiitk50
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Is there gold standard data for ancestral reconstruction?
... Is there gold standard data for ancestral reconstruction? I am asking because I am trying to create a new approach for ancestral (gene/protein sequence) reconstruction (using a algorithm that has not been used before for this) and I wanted to compare the performance of current tools like MrBayes, ME ...
gene evolution phylogenetics protein written 4 weeks ago by chahatupretiiitk50 • updated 22 days ago by Jean-Karim Heriche15k
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Comment: C: GTF2BED does not provide meaningful output?
... Hi Alex, But as I mentioned in my question (the 2 lines I copied from the gtf), the `transcript_id ` **is** present in the gtf. Also, what could be the reason that even the example gtf file provided in the website (foo.gtf) also generates an empty bed file? ...
written 5 months ago by chahatupretiiitk50

Latest awards to chahatupretiiitk

Student 6 months ago, asked a question with at least 3 up-votes. For Low mapped percentage. How to know if data is junk?
Supporter 6 months ago, voted at least 25 times.

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