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Questions tagged [bioinformatics]

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

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2answers
20 views

Does the brain have a clock and can it be sped up?

Before i start, I'm an engineer and have very limited knowledge on biology and neuroscience. My question is, does the brain have a clock like a computer where it has a set processing speed? Clocks in ...
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0answers
9 views

What software is good for the Y STR data processing?

What software is good for the Y STR data processing? I have Arlequin, Structure, GeneLand and Cervus. What is a better choice for the data processing of haploid Y STR data for the estimation of a ...
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0answers
10 views

what is the difference between computational biology and systems biology? [on hold]

If a person creates a discrete time model or a stochastic model of a genetic circuit, which of the above two will this work be associated to?
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0answers
8 views

What parameters of a blast file are appropriate to detect the real positives

I am analyzing the NGS results. I don't know what parameters of a Blast file I should choose to filter the positives: ...
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0answers
20 views

Ligand categories on CAMEO-LB

I'm currently working on methods for predicting binding sites and I wanted to benchmark it with CAMEO, but I'm not really understanding how the prediction should look like. This is a section of the ...
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1answer
23 views

Amino acid substitutions near the receptor binding site HA protein in type A H3N2 influenza strains?

I have read the scientific paper, "Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution" by Björn F. Koel et al (http://science.sciencemag.org/...
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1answer
43 views

What does it mean by “end effects can be ignored”

I have been reading a book ( Statistics for Biology and Health) and i encountered many of following bold text. Consider a long DNA sequence of length N, where N is assumed to be so large that end ...
2
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1answer
52 views

Gene vs Protein homology

I am trying to find homologs for some proteins and I am wondering if it is better to find it by comparing the proteins or the coding genes or either is fine.
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1answer
21 views

Observed to Expected CpG

Observed to Expected CpG is calculated as below : Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. I also don't ...
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0answers
75 views

Are evolutionary algorithms calculated in polynomial time? [closed]

How complex are evolutionary algorithms? Also, what is the relationship between variational principles (Lagrangians, minima and maxima,) and evolutionary algorithms? Basically, how hard is it right ...
2
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3answers
97 views

Strand representation in the DNA version of the Genetic Code

A Wikipedia entry entitled DNA Codon Table states that the codons presented in the table are on the ‘sense strand of the DNA’. But what is the purpose of this, if the sense strand doesn’t code for ...
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1answer
21 views

How does one predict how large of an effect on antigenic drift a substitution in the amino acid sequence of a surface protein of influenza has?

I know that some amino acid substitutions are more effective in causing antigenic drift than other substitutions based on their location in the 3d structure of the HA protein (proximity to the ...
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0answers
22 views

Brownian motion : Understanding the output of mvBM function.?

To fit the brownian motion for independent evolution of traits i used below code: ...
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1answer
42 views

GC content of a protein-coding region

I have computer science background and I am trying to understand the equation below. The average value of the G + C content of a protein-coding region is given by : (G+C)= $\sum_{\alpha} (I_\alpha *...
3
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2answers
53 views

Difference between NCBI's /genomes and /1000genomes

Wondering what the difference is in the data hosted here: ftp://ftp-trace.ncbi.nih.gov/1000genomes ftp://ftp.ncbi.nih.gov/genomes/ Also (sidenote), would be interested to note what the difference ...
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1answer
114 views

Programming Languages for Bioinformatics [duplicate]

Good day everyone, I am very much interested in math, biology, and programming; ideally I would like to study bioinformatics and, as such, was wondering what languages are typically used by ...
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0answers
13 views

Agrobacterium tumefaciens risks vs effectiveness

Are there genes in Agrobacterium that are analogous to lacZ found in enteric bacteria, and if so what genes are they. Does A. tumefaciens have orthologs for starch and glucose use? How risky is ...
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1answer
25 views

Can I simulate a previous and next sequence of my fasta files?

I have fasta sequences of a virus protein that had suffered a mutation in 2008 and this mutant had increase it fitness when compared to wild strain (according to literature).I want to simulate if my ...
3
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2answers
114 views

How are cell death like apoptosis and entropy related?

In Perspectives on Statistical Thermodynamics, Yoshitsugu Oono, it is written that Do not conclude, however, that since the second law is invincible, information thermodynamics is unimportant. It ...
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1answer
28 views

How to set the phenotype in GWAS analysis?

In the GWAS analysis, my animal sample phenotype is whether an individual dies or survives. And I have every sample death time. How do I set the phenotype in GWAS analysis?
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0answers
27 views

How to calculate the phase of a split CDS?

I am trying generate a custom general feature format (GFF) file but I need to calculate the phase of the Coding Sequence (CDS). This phase is a concept that I haven't grasped. To calculate it, I have ...
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1answer
30 views

identification of differentially expressed genes in RNA-seq analysis

I am using four different packages (viz. EBSeq, DESeq2, edgeR, LPEseq) for identification of differential genes. Now I am confused whose fold change value should I take for further downstream ...
0
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2answers
33 views

why and how multi allele gets reported during variant calling in vcf?

This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can ...
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1answer
44 views

What do these novel splicing sites mean?

I'm sure that the anwser is obvious for some of you but I just endend my internship where we found novel splice junctions (junctionseq; RNAseq data) (see the attached file) and I have some ...
3
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1answer
30 views

Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?

I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the discussion. The R package 'plotly' enables rendering online-publishable tables ...
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1answer
40 views

How does collaboration on reconstructing metabolic networks work?

I am a researcher in psychology and I am trying to come up with a framework/platform in which psychological phenomena can be studied from a dynamical systems / computational perspective in ...
1
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1answer
76 views

Giga base or Giga byte [closed]

"we reported ~2.66- Gb genome sequence of" "we generated 191.5 Gb high quality reads" I am very confused with these two quoted lines and I am not sure about giga byte or giga base pair. and an ...
4
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2answers
117 views

Can two proteins sharing a few domains be considered homologous?

I wonder when to say two proteins are homolog. In the current example I checked the sequence of these two proteins in pfam and as you see they have some shared domains but all domains are not shared. ...
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0answers
24 views

finding chromosome bands of a list of genes

I have performed a meta-analysis on 6 datasets of bovine microarray data. I need to find the chromosome bands of all differentially expressed genes achieved from the analysis. How can I do that?
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1answer
43 views

Consensus symbols in multiple sequence alignment [closed]

I was using multAlin for multiple aligning a set of sequences. The output I and came across included the following documentation (English corrected): Consensus symbols: ! is any of IV $ is any ...
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0answers
28 views

What can I research for thesis on DNA data storage from math? [closed]

I'm a math researcher, I just finished a Master on Error Correcting Codes. I recently saw a presentation on DNA-based data storage that I loved. I wish to continue my studies on (applied mathematics) ...
3
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3answers
76 views

Biological validation of computationally determined gene-gene interaction

How can a computationally determined three-way gene interaction be biologically validated? What kind of assays or tests must be performed using cell/tissue-based and/or mouse models to prove that the ...
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0answers
26 views

How to calculate the Marker Index(MI) for a dominant marker such as RAPD and ISSR?

I am working in the genetic diversity analysis of a plant species and have used RAPD and ISSR markers. After scoring the data in a binary matrix, I am trying to find the marker index of the primers. I ...
0
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1answer
31 views

Is it possible to re-align of SAM/BAM files?

I am carrying out some metagenomic comparison using whole genome sequencing approach. I would like to filter out reads from my files in a sequential manner, thus I would like to align to a first ...
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0answers
35 views

Use of eigenvalues of Sturm-Liuville operator

I am wondering what would be application in biology where bounds on the Eigenvalues of Sturm-Linville operator would be important?
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0answers
16 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 ...
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0answers
30 views

Progressive Multiple Sequence Alignment: “Add” a sequence to the MSA

I understand the basic steps of progressive sequence alignment: Construct a pairwise distance matrix between all sequences Based on that, construct a guide tree Pick the closest two sequences from ...
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1answer
37 views

gene expression of tumor with different percentage of infiltrates

I'm performing differential gene expression analysis on rnaseq of tumor samples that might have different amounts of immune infiltrate. Tumors are extracted from patients that respond/not respond to ...
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0answers
22 views

primer blast for BSP methylation

How can I blast my BSP(Bisulfite sequencing) primers? I designed in this way that C nucleotide converted to T and my primers just sit on the converted DNA! I blast it with Bisearch but I don't know ...
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4answers
117 views

Program (on Mac) to show 3D protein structures?

I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I’m interested in currently. what I already did I already looked up ...
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2answers
49 views

MLE estimation with Mk model in ape or phangorn?

When doing MLE with the R package ape or phangorn, is it possible to set the substitution model to Mk? If so, how does one do this?
1
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1answer
32 views

Is there a notion of RMSD for two different molecules?

The (least) Root Mean Square Deviation is used for comparing different conformations of the same molecule. However one may be interested in comparing the conformations of two different molecules e.g. ...
3
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1answer
45 views

How to do a blast search for similar sequences?

Tried doing a Blast search for a PPO gene in an advocado genome: https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEFAULTS=on&BLAST_SPEC=OGP__3435__73885&DATABASE=...
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1answer
54 views

How to find a gene sequence?

So I need to learn how to find the sequence of a gene, polyphenoloxidase. Please do not do this for me. Tell me how to approach the problem. I have found : https://www.ncbi.nlm.nih.gov/gene and ...
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0answers
77 views

Why is GenBank growth slowing down?

https://www.ncbi.nlm.nih.gov/genbank/statistics/ shows the growth of the GenBank database is slowing since WGS (Whole Genome Shotgun) emerged. Is this happening because sequencing centers are ...
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1answer
28 views

Tools to find miRNA ID

How can I get accession numbers of bread wheat miRNAs by their sequences? What are the tools or website that can be used?
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1answer
113 views

How to get phased haplotype from vcf file?

Although I'm reading all days and nights, still confused in this area. I have hundreds of BAM files (from whole-genome sequencing of a given human population). I was wondering how I can obtain phased ...
2
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0answers
34 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. ...
1
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1answer
133 views

What's a structural RNAs?

In genbank (ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Fungi/Saccharomyces_cerevisiae_uid128/) there are an archive .frn (nucleotide sequences of structural RNAs in fasta format), and I ...
2
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1answer
36 views

Log-tranformation and GWAS

Before doing any GWAS (genome-wide association study) it is necessary to check for the normality of the phenotypic distribution. If the phenotype is normally distributed only once it is log-...