Questions tagged [bioinformatics]

The science of collecting and analyzing complex biological data such as genetic codes using informatics.

127 questions with no upvoted or accepted answers
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1answer
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Additive genetic variance components from LMER in R

I've set up some dummy data in R which makes 40 genetically related lines, they are all siblings within a line so are genetically related by a factor of ½ thus additive genetic variance should be ...
15
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1answer
313 views

At which step should I apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal)

What is the best practice when preprocessing microarray data using a detection filter (on scanner p-value)? Suppose I have a microarray dataset that I have to normalize with Loess and correct with ...
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77 views

Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
4
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0answers
163 views

Are there any de-novo genome assembly programs for HADOOP?

I have access to a small (approx 20 nodes) cluster that has HADOOP running on it, and I need to do some de-novo genome assembly. I'd like to ask is anyone knows of any program that can do this on a ...
3
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0answers
81 views

Should you perform an ordination (such as PCA) of abiotic variables before a Redundancy analysis (RDA)?

I have a dataset of viral 'OTUs' across various sample points from different sites/times. I also have meta-data collected at these same sample points, for things like temperature and the ...
3
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0answers
103 views

Use of pipe character in VCF info field

While annotating my VCF file with ClinVar, I noted the following value for the CLNSIG field (i.e., clinical significance): ...
3
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0answers
90 views

Reduce protein structure representation dimensionality.

In my lab we are trying to extract spatial features from protein structures. The software we develop makes use of CUDA for all heavy number-lifting, thus we are limited by the GPU's memory (12GB). ...
3
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0answers
139 views

Haploview command line: how to get tagSNP

I am trying to use Haploview command line software to compute haplotypes and extract tagSNP for those. When I use the standalone version on my local computer I tick the 'Show tags in blocks' option so ...
3
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0answers
118 views

How can I create R8 (homopolymer repeat) filter without using illumina pipeline?

illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and ...
3
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0answers
605 views

Accuracy of genome size estimation by flow cytometry

I'm working on a genome project and using an in silico k-mer analysis to estimate the size of our genome based on the available Illumina reads. The k-mer based estimate is consistent across a wide ...
3
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0answers
166 views

Good poly-A filtering rules or tools

I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have ...
3
votes
1answer
232 views

How to interpret Glimmer scores?

I am trying to find orfs with Glimmer. At the end, Glimmer gives me a .predict file with the orfs and a corresponding raw score. When I look at the documentation, it says about the score, "This is ...
2
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1answer
81 views

Extract mutations from fasta sequences

I have a large amount of protein sequences in the .fasta format and I would like to extract only the amino acid mutations from these sequences, so that, in the end, I want to have a list that looks ...
2
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0answers
131 views

Why do BRAF mutations appear more in skin cutaneous melanoma?

When looking at the tissue expression of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. There is elevated expression in tissues like the Testis and the ...
2
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0answers
69 views

Brownian motion : Understanding the output of mvBM function.?

To fit the brownian motion for independent evolution of traits i used below code: ...
2
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0answers
45 views

totaling OTU from 2 or more observations and assign to new observation in OTU table from qiime

I am new to microbiome processing pipeline but I want to ask, How do I combine two observations and assign it to a new single observation in the OTU table resulted from QIIME. Here is the situation. ...
2
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0answers
125 views

Protein/ligand affinity databases?

Is there any database that contain binding affinities reported in litterature for different proteins and ligands? I have checked uniprot already and it does not seem to included any binding affinity ...
2
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0answers
74 views

Basic molecular biology of nucleic acids book for a mathematician studying DNA and RNA formally?

I am a mathematician studying DNA and RNA language from the perspective of Formal Language Theory. Note that I am aware of these posts: best book for a comprehensive introduction to biology for a ...
2
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0answers
62 views

How to evaluate broad-sense heritability of microbiome associated plant genotypes in R

I have a data containing 196 accessions of A. thaliana from which I studied leaf bacterial and fungal community and, therefore, sequenced and found several OTUs. Now, I want to evaluate broad-sense ...
2
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0answers
388 views

what is the meaning of the genotype values in each snp

I understand that snp is a single base variation. For example, if person 1 has the sequence in DNA , AAGCCTA the second has AAGCTTA, then the allels are C,T. My question is what is the meaning of 0,...
2
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0answers
498 views

What's the best wat to combine biological replicates in qPCR gene expression analysis? (2^(-∆∆Ct) method; one-way anova, turkey's test)

I am measuring the levels of gene x after transfection of cells with a plasmid and I want to compare them to the levels in mock-transfected cells. I did three different transfection experiments, in ...
2
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0answers
55 views

Are there any examples of weighted edit distance genome alignments?

It has been said that weighted edit distance is a preferred way to compare/align genomes in practice, e.g., when identifying genetically similar patients. I wonder if there are some concrete examples ...
2
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0answers
70 views

PCR limits of detection calculate method

Is any standard method for use to gain PCR sensivity or limit of detection? my mean is not for RT-PCR or Real-Time or any other kind and just simple PCR. After making PCR product free of dNTP and ...
2
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0answers
74 views

Kegg in Cytoscape: how to get plots with reaction IDs in place of EC numbers using KeggScape?

I found a KeggScape manual page representing Kegg reactions in Reaction ID format, but I couldn't find how to get a Kegg plot with reaction IDs in place of EC numbers. Does anyone know?
2
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0answers
58 views

Finding diploid neanderthal alignment data, looking for ambiguity codes

I'm using Neanderthal alignment data from here: http://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html Specifically, the .bam files. I would like to find alignments for neanderthal ...
2
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0answers
49 views

Looking for dataset of proteotypic and non-proteotypic peptide

I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science. Any advice how to find proteotypic and non-proteotypic peptides....
2
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0answers
62 views

What is the best test for SNV clustering?

I am looking for a method to cluster single nucleotide polymorphisms based on clinicopathologic data (mainly receptor immunoistochemistry). So far, I've came up with only two that handle dummy ...
2
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0answers
119 views

Efficient algorithm to calculate various population divergence statistics

Intro and description of the data I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format ...
2
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0answers
80 views

How to characterise a protein family in a putative genome island?

We have sequenced the genome of 200 bacterial strains belonging to the same species, a swine bacterial pathogen. In a previous work, it was observed that a protein family of adhesins is present in ...
2
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0answers
166 views

Biology Experiment Data (Hodgkin-Huxley)

I'm doing research into the Hodgkin-Huxley Model from an electronics/mathematics perspective and I'm looking to find actual numerical results from experiments on squid axons. I want to compare the ...
2
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0answers
64 views

Genome-wide methylation analysis: sources of technical error?

We are doing a genome-wide analysis of methylation via bisulfite sequencing for an insect species. Previous experimental techniques have suggested the presence of methylation in this organism, ...
2
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0answers
127 views

dbSNP database table desciptions

I am trying to build a local implementation of dbSNP. I would like to know the descriptions of tables listed on ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606 and on ftp://ftp.ncbi....
2
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0answers
68 views

Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?

E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms ...
2
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0answers
111 views

Reverse complement of reconstruction model for assembling reads

One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
2
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0answers
210 views

Too few transcripts from transcriptome assembler Oases

I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks. Here is my running command: ...
1
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0answers
33 views

NCBI blast for exact match of short sequence

I'm trying to Blast for exact matches to the sequence: 'ATTGNNNNGCAAACCA' in the human transcriptome using NCBI Blast on its 'refseq_rna' database. However, when I do a basic query I get "No ...
1
vote
1answer
30 views

Help Finding Specific BlaZ Gene Type Sequences on Genbank

I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that ...
1
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0answers
45 views

How large a part of the corona-virus is coding?

If you find an example of a sequenced string of coronavirus it is about 30.000 long. Looking for example here https://nextstrain.org/ncov/europe you'll see that by far the largest part of this is ...
1
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0answers
55 views

Can two proteins activate/inhibit the same gene at the same time?

Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right? So if one protein has already inhibited that gene before ...
1
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0answers
19 views

Where can I find and download HMMTOP training set?

I would like to perform redundancy reduction for my test set for membrane topology prediction. I checked the 1998 paper and website of the HMMTOP server but haven't found any download links for the ...
1
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0answers
16 views

Is there a measure for degree of reticulation in a phylogenetic network?

When working with phylogenetic networks, how does one talk about reticulate (i.e., web-like) the branches are? Is there a standard measure of this?
1
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0answers
19 views

Is there any data to explore the heterozygosity of the South African lion over the last 18 years?

Background: I need to find data on the heterozygosity of the south African lion over the last 18 years... and I'm struggling: so far I have found a single data point. Question: Where can I find ...
1
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0answers
23 views

Database of predicted protein-ligand binding/docking score

Is there a database of computationally determined "binding scores" across protein-ligand pairs in the PDB? My phrase "binding score" is deliberately generic, since any such score would be fine. In ...
1
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0answers
30 views

How does one calculate Rx/a in population genetics?

The ratio of sex-linked to autosome mutation frequencies (R) is Rx/a =(2/3)(2+ α)/(1+ α) for X-linked genes and Ry/a = 2 α /(1+ α) for Y-linked genes. How does one calculate Rx/a, in order to find α?
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0answers
226 views

How to correlate survival probability to gene expression profile?

I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how ...
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0answers
24 views

Characterising mechanisms responsible for generating structural variants

I have a high-quality set of structural variant breakpoints from tumour/normal WGS data, and I am interested in digging into the various mechanisms that might be involved in each event. There are ...
1
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0answers
330 views

What is a proper software to do GWAS analysis of tuberculosiis VCFs and phenotype data?

What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association ...
1
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0answers
79 views

The advantages of using a strand specific cDNA in RNA-Seq?

May I ask what are the advantages of using a strand specific cDNA library in an RNA-seq experiment? as far as I know it can make us able to read the code region but what about other advantages?
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0answers
32 views

Fisher's Method to melt p-values for CpG sites annotated to the same gene?

I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
1
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0answers
21 views

What are the chemicals of betel leaves that may react with estrogen?

Im conducting this experiment about pregnancy testers.Im not quite sure what extract method i can use regarding this experiment.any thoughts?? please help me..