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

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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 &...
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1answer
19 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 ...
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1answer
22 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
25 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 ...
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1answer
51 views

Giga base or Giga byte

"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
85 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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18 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
27 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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13 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
25 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
45 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
17 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
24 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
28 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
14 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
21 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
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
9 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
94 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
43 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
30 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. ...
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1answer
42 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
48 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
67 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
24 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
48 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 ...
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0answers
28 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. ...
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1answer
60 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
31 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
23 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
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1answer
35 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
10 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 ...
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1answer
40 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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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
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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....
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1answer
32 views

Can you do DNA seq with Microarray? [closed]

Is it possible to do the entire DNA sequencing with Microarray or would you have to use Sanger or NGS methods for that?
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1answer
122 views

determining horizontal gene transfer between two genomes?

I want to determine if there is horizontal gene transfer between two genomes, in particular I was to use the parametric methods described in wikipedia since I would most likely struggle to understand ...
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0answers
13 views

How is heritability calculated for an asexual population?

Do I have this calculation correct for the heritability of fitness for an asexual population? (FYI, this is an example of my own, not any sort of a HW question.) One specific concern is, when ...
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0answers
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Only 1 rDNA sequence in a diploid organism… how it is possible?

While molecular identification of an organism, such as a plant, we commonly send the isolated DNA to some other departments or institutes, who gives a DNA sequence (rDNA(5s/5.8S/28S/18S) or ITS(1/2) ...
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2answers
49 views

moltype controlled vocabulary?

In submitting sequences using tbl2asn to NCBI/GenBank, the documentation states that there is a controlled vocabulary for the key "moltype", but no where on the Internet can I find a full list of that ...
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32 views

Test significance between Single Cell Clusters

I'm doing some data analysis on small set of cells (only 67 after filtering) which can be reasonably divided into 3 clusters from different organs. They are clearly distinguishable after both ...
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0answers
14 views

How to find the UTR sequences in yeast?

Since it is know that the promoter say for example GAPDH promoter does not contain 5'UTR sequences, so from where we can take the UTR sequences of any gene????
2
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1answer
28 views

Is there a simple way to generate sets of sequences that re-capitulate the topology of pre-defined phylogenetic tree

I would like to generate ensembles of N sequences in such a way that the phylogenetic trees obtained from my ensembles (e.g., by neighbor joining) have the same (or nearly the same) topology as a ...
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1answer
71 views

Where does DNA fit on the Chomsky hierarchy? [closed]

Since adenine pairs with thymine and guanine pairs with cytosine, this seems to imply that there's a trivial Regular Expression for DNA (i.e. it's trivially a Regular Language, which is Type 3 on the ...
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1answer
43 views

Genetic modifications in humans to prevent disease [closed]

I was reading an article about "designer babies", which was about how before birth the DNA can be modified so to achieve certain features. Can a technique such as this also be used to prevent diseases,...
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3answers
53 views

Is there any way to tell if a gene is functional for an individual with only a reference sequence and the individual's sequence of the gene?

I have gene sequence of a ton of individuals within a subspecies from cdna and the ncbi IDed sequence as well. Is there any way to tell using just the sequence that the gene for an individual is non-...
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0answers
23 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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How to find a novel antibiotic resistant gene in my bacterial strain?

I'm a Msc student here. My project is to test the antibiotic susceptibility of abscessus strains, and then use WGS to find for the genes that cause the resistance. Here is where i got stuck as i have ...
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36 views

How much Open Access Data is there in genetics?

Type of data of interest I would like to consider Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...) Genetic - phenotype data (disease-related data, QTL, etc...) Sequence ...