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

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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 *...
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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?
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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.
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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 ...
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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 ...
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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 ...
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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 ...
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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
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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 ...
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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?
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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
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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 ...
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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
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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 ...
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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
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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
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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 ...
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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
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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 ...
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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. ...
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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
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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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 ...
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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?
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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 ...
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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
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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 ...
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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
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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 ...
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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?
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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
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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=...
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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
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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 ...
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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?
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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
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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
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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-...
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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 ...
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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 ...
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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 ...
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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
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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.
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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....
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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....