User: '

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'160
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Comment: C: Gene (mRNA) - Protein Interaction databases and prediction
... That's exactly the aim: predict computationally (for example RNA-binding capabilities between those proteins and the gene of interest), and if the result is reliable, start an experiment. Are there any known approach to do the prediction? ...
written 8 months ago by '160
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Answer: A: Normalized Smith-Waterman similarity score based on pairwise amino acids sequenc
... Here's a naive approach: library("Biostrings") library("seqinr") ## Load protein sequences #Protein_Seq <- read.fasta("Protein_sequneces.fa", seqtype="AA", as.string="TRUE") #Protein_Sequences_Only <- getSequence(Protein_Seq, as.string=TRUE) data("BLOSUM62") ...
written 8 months ago by '160
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Gene (mRNA) - Protein Interaction databases and prediction
... I have a set of proteins and I want to find out how they interact with a particular gene. Are there any tools and/or databases that would be suitable for this purpose? ...
gene mrna ppi protein databases written 8 months ago by '160 • updated 8 months ago by c.chakraborty110
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Comment: C: Classify, organize, and cluster a list of proteins / discovering relations betwe
... "P06909", "Q3UV17", "P07724", "Q61147", "Q6ZPJ3", "P20918", "Q7TT37", "Q62469" ...
written 8 months ago by '160
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Comment: C: Classify, organize, and cluster a list of proteins / discovering relations betwe
... Fixed now. It was a mistake. ...
written 8 months ago by '160
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Classify, organize, and cluster a list of proteins / discovering relations between a set of proteins and linking them to disease
... I have a list of proteins (only `Uniprot IDs`) and I am interested in discovering relations between them. Most importantly I want to focus on disease pathways and find out whether the proteins I am looking at are part of particular disease(s). Additionally, functional relations, pathway analysis, ...
cluster protein written 8 months ago by '160
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Answer: A: NCBI blast remote on specific species
... I know this is an old thread, but it took me a long time to figure out the same---this stuff is not well-documented. So I want to post an answer to this thread to clarify how one can achieve what's asked for in this thread (both the remote and local way). I am using the latest version of **BLAST+** ...
written 13 months ago by '160
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Comment: C: Europe: Non-Paid Bioinformatics Internships/Training
... To people reading this thread in the future, don't take the guy above seriously. ...
written 13 months ago by '160
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Comment: C: Normalized Smith-Waterman similarity score based on pairwise amino acids sequenc
... I ended up using `R` which was reasonably fast for my limited computational resources. I used `Biostrings::pairwiseAlignment`. ...
written 14 months ago by '160
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Comment: C: Is PatScan RNA pattern searcher no longer available as an online webtool?
... Yes, @b.nota, you are absolutely ignorant and self-righteous and I am not going to take it back because the internet is rife with arrogant people like you who think they are the best in everything and people like you should disappear from the face of the internet or just keep their mouth shut. And y ...
written 18 months ago by '160

Latest awards to '

Popular Question 11 months ago, created a question with more than 1,000 views. For Training and/or Master's Thesis at EMBL Heidelberg
Popular Question 11 months ago, created a question with more than 1,000 views. For Understanding Kernel Ridge Regression for Drug-Target Interaction
Popular Question 11 months ago, created a question with more than 1,000 views. For Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 11 months ago, created a question with more than 1,000 views. For How to interpret MUMmer plots? When do you know that your alignment was a good one?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to model transcriptional networks from gene expression time-course data
Popular Question 13 months ago, created a question with more than 1,000 views. For Training and/or Master's Thesis at EMBL Heidelberg
Scholar 13 months ago, created an answer that has been accepted. For A: How to model transcriptional networks from gene expression time-course data
Popular Question 13 months ago, created a question with more than 1,000 views. For Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 18 months ago, created a question with more than 1,000 views. For Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 24 months ago, created a question with more than 1,000 views. For Europe: Non-Paid Bioinformatics Internships/Training
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: How to model transcriptional networks from gene expression time-course data
Supporter 2.4 years ago, voted at least 25 times.
Scholar 2.8 years ago, created an answer that has been accepted. For A: How to model transcriptional networks from gene expression time-course data

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