Community Digest

Top new questions this week:

Comparing phylogeny in R

So I want to compare the phylogeny created using two methods for example Maximum likelihood and maximum parsimony.Is there any way to compare the two phylogeny ? I did read about phangorn but not ...

r phylogenetics  
asked by krushnach Chandra 2 votes
answered by thomas duge de bernonville 2 votes

Where can I visualize Ramachandran plot?

I am using Rampage webserver to obtain a Ramachandran plot. However, the server does not reveal any plot just values (favored, allowed, outlier regions). Can you recommend other similar web sites?

3d-structure validation  
asked by polonio210 2 votes
answered by Maximilian Press 4 votes

Edit FASTA header using sed

I need to rename the following headers from a FASTA file. Something like: >ENST00000488147.1::chr1:29570-30013(-) >ENST00000405392.5::chr2:24919186-24920186(-) into different format like ...

fasta bash linux  
asked by taeju 1 vote
answered by ATpoint 5 votes

setting BLAT alignment parameters to give long matches

I'm using BLAT to align DNA sequences between similar species, and having trouble setting the parameters to return only significant matches along the 50bp query lengths. Using -tilesize=11 ...

sequence-alignment blat  
asked by Joanne 1 vote

Very low probability densities

I'm generating a density plot using the ggplot2 library: ggplot(df_chr20, aes(x=start1)) + geom_density() + theme_bw() ggplot(df_chr21, aes(x=start1)) + geom_density() + theme_bw() The data frame ...

r statistics ggplot2  
asked by rishi 1 vote
answered by StupidWolf 2 votes

Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?

I manually selected all 4000 sequences on the 20 pages of the SARS-CoV-2 sequences on genbank here. When I click on Build phylogenetic tree, it only has 200 nodes. Is this expected? I was expecting ...

phylogeny genbank  
asked by shadi 1 vote
answered by Michael 1 vote

Available Protein sequence alignment dataset and HMM model

It may better to move the question here. I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to ...

sequence-alignment proteins sequence-analysis machine-learning hidden-markov-models  
asked by Qinsheng Zhang 1 vote

Greatest hits from previous weeks:

Why do NEBNext indexing primers have sequence between the p5 oligo and index?

In a previous post I asked Why do NEB adapters have non-complementary sequence? Since then, I realized that there is some other sequence in the p5 indexing primer, as well as in the p7 indexing ...

dna illumina adapter pcr library  
asked by conchoecia 4 votes
answered by Beth Nelson 4 votes

Set directory where MinKNOW writes FAST5 files

I would like to set the folder in which MinKNOW writes the raw data. How can I do this? I do not currently know where MinKNOW will output my data. What is the default directory where MinKNOW outputs ...

nanopore sequencing minion minknow  
asked by charlesdarwin 1 vote
answered by 719016 2 votes

Is it possible for coronavirus or SARS to be synthetic?

I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant of Middle ...

fasta phylogenetics sequencing protein-structure phylogeny  
asked by Sscheme 13 votes
answered by Michael 21 votes

How to append numbers only on duplicates sequence names?

I have a reference database with contains 100s of sequences in fasta format. Some of these sequences have duplicate names like so: >1_uniqueGeneName atgc >1_anotherUniqueGeneName atgc ...

fasta text  
asked by AudileF 5 votes
answered by terdon 5 votes

SNP vs Point Mutation

What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the ...

snp terminology variation  
asked by Zheng Keong Ng 5 votes
answered by finswimmer 4 votes

Can open-source software be peer-reviewed and published?

My colleague and I have developed a software tool intend to release it open-source. This tool is specifically for tasks in bioinformatics but we think it would be helpful for the wider community. Our ...

software-development publishing  
asked by Tom Kelly 11 votes
answered by Devon Ryan 12 votes

How to calculate p-values for fold changes?

I'm currently working with data from a Luminex multiplex assay. In this assay, the concentrations of 17 different analyte proteins were identified in 12 groups in triplicate. One of these 17 groups ...

asked by J0HN_TIT0R 3 votes
answered by Devon Ryan 3 votes
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