Questions tagged [bioinformatics]
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
3
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2answers
76 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 ...
0
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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 ...
0
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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?
0
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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:
...
0
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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 ...
0
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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/...
1
vote
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
votes
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.
0
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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 ...
2
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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
votes
3answers
98 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 ...
1
vote
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 ...
2
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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:
...
0
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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
votes
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 ...
0
votes
1answer
120 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 ...
0
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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 ...
0
votes
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
votes
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 ...
0
votes
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?
-1
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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 ...
1
vote
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
votes
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 ...
0
votes
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
votes
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 ...
0
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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
vote
1answer
77 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
votes
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. ...
0
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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?
1
vote
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 ...
1
vote
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
votes
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 ...
0
votes
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
votes
1answer
33 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 ...
0
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0answers
36 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?
1
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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 ...
0
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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 ...
1
vote
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 ...
0
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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 ...
5
votes
4answers
121 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 ...
1
vote
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
vote
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
votes
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=...
0
votes
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 ...
3
votes
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 ...
0
votes
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?
1
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1answer
115 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
votes
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
vote
1answer
134 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
votes
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-...
