User: virpatel3

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virpatel320
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Posts by virpatel3

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Comment: C: Filtering by specific genotype VCF
... So 274 samples in 1 VCF. If there is a heterozygous site, I'd like to remove it, with the distinction of ./. as is typically prescribed for sites without data. You see, this is genotype data for a malaria strain, which is haploid. ...
written 9 weeks ago by virpatel320
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Filtering by specific genotype VCF
... I have a vcf file with 274 samples in which I need to remove all heterozygotic SNPs for individual samples, since I am studying a haploid model. How can I best accomplish this? ...
vcf filter genotype written 9 weeks ago by virpatel320 • updated 10 days ago by agata88610
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Secondary Structure Alignment Method
... I have many genes for many bacteriophage with precomputed secondary structures such as:   HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCHHHHHHHH I want to align each gene's secondary structure with the SSE (secondary structure elements) of the other bacteriophages. So for instance, I may a ...
alignment structure secondary written 2.5 years ago by virpatel320 • updated 2.5 years ago by a.polo88100
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PSSPred Alignment Alignment
... PSSPred gives me wonderful data of protein secondary structures. For instance, I have  HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCHHHHHHHH for one part of my prediction. I want to perform an alignment with this data, but I am quite unsure as to what would be the best algorithm. Any sugg ...
i-tasser psspred alignment written 2.5 years ago by virpatel320
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Convert to PDB Format from Secondary Strucutre
... I have a sequence of secondary structures in the following format: CCCCCCCCHHHHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHH     I also have the amino acids underneath these structures. Is there any way I can convert this information to the PDB format?     ...
pdb secondary convert structure written 2.5 years ago by virpatel320 • updated 8 months ago by Biostar ♦♦ 20
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RaptorX Alignment Method
... I have about 400 bacteriophage genomes. For each bacteriophage, I have computed the secondary structures for each gene using RaptorX.    RaptorX uses a probabilistic method to calculate secondary structure. So for each amino acid, a probability is given for 8 structures.  For instance, the 16th a ...
alignment secondary algorithm raptorx structure written 2.5 years ago by virpatel320
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GenBank Batch Download
... I have a list of bacteriophage names. A program that I am using would like the GenBank entries for all of these phage. For instance: http://www.ncbi.nlm.nih.gov/nuccore/339754473 Now, there is the option to download all of these by hand using the Send feature. But is there a second, faster way to ...
nucleotide e-utilities entrez genbank download written 3.0 years ago by virpatel320 • updated 3.0 years ago by 5heikki6.5k
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Periods of microRNA Innovation
... I have a set of microRNA ages with corresponding labels suggesting which clade they first emerged from. For instance, for hsa-mir-1, let's say, it would have an age of Eutheria. I have several peaks in the distributions of my age. One idea I had was to check to see if these peaks correspond to perio ...
diversity phylogenetics evolution microrna written 3.1 years ago by virpatel320

Latest awards to virpatel3

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Secondary Structure Alignment Method
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Convert to PDB Format from Secondary Strucutre
Popular Question 2.4 years ago, created a question with more than 1,000 views. For GenBank Batch Download

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