The science of collecting and analyzing complex biological data such as genetic codes using informatics.
0
votes
1answer
29 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 *...
0
votes
0answers
10 views
Sorting by Prefix Reversal (or Flipping Pancakes) approximation
Does anyone know how to prove that the Sorting by Prefix Reversal (or Flipping Pancakes) is a 3 as well as a 4-approximation?
-6
votes
0answers
37 views
Ramachandran Diagram [on hold]
1)Explain briefly their(Ramachandran Diagram) importance in studying biological systems.
2)Explain the terms present in a classical Molecular Mechanics energy equation.
0
votes
0answers
25 views
Genomics: Downloading genomic data from the NCBI Genbank database
I'm taking a genomics course at school, and we have a final project due in a few weeks.
Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually ...
3
votes
2answers
48 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
41 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
votes
0answers
10 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
24 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
83 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
26 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?
0
votes
0answers
23 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
27 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
0answers
16 views
sample coverage based rarefaction with Hill numbers
I am trying to apply the coverage-based rarefaction approach with Hill 1 and Hill 2 based on the research article below (1). The sample coverage standardizes assemblages not by sample size but sample ...
0
votes
1answer
20 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
0answers
29 views
Global alignment with one sequence larger than another
If a sequence α is much larger than β, then is there an optimal global alignment between α and β that does not add gaps in α? Considering an alignment scoring scheme such that gap ≤ mismatch < 0 &...
0
votes
1answer
32 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
29 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
votes
1answer
35 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
59 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
93 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
votes
0answers
21 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
34 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 ...
0
votes
0answers
14 views
Identifying the time window at which a meteorological factor influences tree growth the most
This is a problem I am encountering in a research project. I have thought of a naive approach to solve it which relies on many assumptions, is not guaranteed to work, and would be tedious and ...
1
vote
0answers
26 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) ...
2
votes
2answers
62 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
22 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
26 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
votes
0answers
34 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
vote
0answers
15 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
votes
0answers
23 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
36 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
votes
0answers
11 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
101 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
47 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
31 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
44 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
50 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
72 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
26 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
vote
1answer
80 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
30 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
79 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
32 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-...
0
votes
2answers
52 views
How to determine which is the nucleotide sequence of a gene?
I have came across a few genes that show different nucleotide sequence in different databases. I then found out that the sequences are actually reverse complement of each other. How do i determine ...
0
votes
0answers
24 views
Statistical Genetics - What information is required for haplotype phasing in a novel, admixed population?
Let's say there is a population that has never been sequenced before and has experienced varying levels of admixture from multiple sources at different times. There is ancient admixture and recent ...
2
votes
1answer
37 views
What does “This variant falls on 11 transcripts in 3 genes” mean in the output from GnomAD?
The gnomAD browser provides information on variants of genes (in this link, for the SAMD11 gene.) The report on a particular variant, like this one, includes the information in the header that says ...
1
vote
0answers
12 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 ...
0
votes
1answer
45 views
What is meant by Gene Expression Level?
I am new to BioInformatics, I want to know what is gene expression level and how it is determined.. Anyone who can answer this silly question.
0
votes
0answers
19 views
Calculating heritability, additive variance and total variance from a simulation
I have written a program intending to test a couple of evolutionary strategies and I have calculated heritability for the population (asexual) based on the values recorded during the simulation itself....
0
votes
0answers
15 views
Is my heritability implementation for an asexual population wrong?
I have written a program intending to test a couple of evolutionary strategies and I have calculated heritability for the population (asexual) based on the values recorded during the simulation itself....
