User: Selenocysteine

gravatar for Selenocysteine
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Dublin, Ireland
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Posts by Selenocysteine

<prev • 75 results • page 2 of 8 • next >
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Comment: C: Ultrametric tree in ete3 (python)
... Thanks, so there is not existing method. It would be a good idea to add one I guess. ...
written 2.8 years ago by Selenocysteine600
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Ultrametric tree in ete3 (python)
... Hi all, does anyone know how to check if a tree has been correctly converted to ultrametric with ete3 in python? Kinda like the is.ultrametric() function of the R ape package? Thanks! ...
phylogeny python written 2.8 years ago by Selenocysteine600 • updated 2.8 years ago by jhc2.9k
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Answer: A: Removing all stop codons from sequence using Biopython
... Bastien is right, there are many unclear points in your question (is the sequence already in frame? Do you want to remove the whole codon or just 1 nucleotide?) etc. Assuming that your sequence is already in frame you can do this: from Bio.Seq import Seq from Bio import SeqIO from Bio.S ...
written 2.8 years ago by Selenocysteine600
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Answer: A: eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer's diseas
... To perform an eQTL analysis you also need genotypic data :D If you have that, you can do it using RNA-seq data. ...
written 2.8 years ago by Selenocysteine600
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Answer: A: high-throughput domain discovery
... Hmmer + Pfam http://hmmer.org/ http://pfam.xfam.org/ ...
written 2.8 years ago by Selenocysteine600
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Answer: A: Python script error
... I think that the issue is that you are trying to translate outside from the for loop, and also that you are trying to translate the output of print instead of the seq item. Try this: import sys from Bio import SeqIO from Bio.Tools import Translate from Bio.SeqIO.FastaIO import * ...
written 2.9 years ago by Selenocysteine600
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Comment: A: I made a DNA/gene/bioinformatics-y workshop for 11-16 year olds which people may
... This is amazing! I think I will use this as an input for the workshop I am organising. Just a question: where can I find the models for the 3d prints? Thanks a lot! ...
written 2.9 years ago by Selenocysteine600
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Pfam/Hmmer redundant annotations
... Hi all, I am annotating some protein sequences with Pfam domains using Hmmer3, and I have noticed that if there are multiple domains with a closely related, very similar, profile, Hmmer will just return a hit for all of them, instead of going for the most specific one. Does anyone have a good way t ...
pfam annotations hmmer written 3.0 years ago by Selenocysteine600
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Answer: A: how to automate microarray data analysis
... You need to check some basic programming tutorials about for/while cycles. This is key to use any type of (pseudo)-programming language. This being said, you can do something like this (I have not checked if it actually works because you did not provide data): # Removes the control column ...
written 3.1 years ago by Selenocysteine600
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Answer: A: Difference between genomes in circular graph
... You can use this tool which is based on CIRCOS, but easier to use if you are not very proficient with coding stuff: http://omgenomics.com/circa/ ...
written 3.1 years ago by Selenocysteine600

Latest awards to Selenocysteine

Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Keeping pheatmap colour range the same for different data sets
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Retrieving clinical trial data using R program
Scholar 3.1 years ago, created an answer that has been accepted. For A: Unusual pyramid plot helpin R or matplotlib
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Retrieving clinical trial data using R program
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Retrieving clinical trial data using R program
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Best tool for generating a phylogenetic tree based on gene sequences
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Genome-wide homology human versus mouse
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Best tool for generating a phylogenetic tree based on gene sequences
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Inferring pedigree from SNP genotyping data
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Retrieving clinical trial data using R program
Supporter 4.5 years ago, voted at least 25 times.
Scholar 4.5 years ago, created an answer that has been accepted. For A: Bio.SearchIO.HmmerIO only showing the best score domain
Scholar 4.5 years ago, created an answer that has been accepted. For A: Bio.SearchIO.HmmerIO only showing the best score domain
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Retrieving clinical trial data using R program
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Genome-wide homology human versus mouse
Scholar 4.7 years ago, created an answer that has been accepted. For A: Bio.SearchIO.HmmerIO only showing the best score domain
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Retrieving clinical trial data using R program

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