Questions tagged [bioinformatics]

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

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26 views

what are the nodes and edges in gene regulatory networks

I am trying to find out how one can using gene expression data can infer gene regulatory network applying graph theory concepts. But I could not find a proper reference that 1)explain how one can get ...
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1answer
108 views

What do the colors mean in representations of amino acids?

I've seen sequences of amino acids depicted using colors, which I imagine correspond to whether the side chain is charged, etc. I can't figure this out, though, and I'm not a biologist or biochemist. ...
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Are there any biometrics that can measure tiredness (sleepiness)?

Are there any biometrics that can estimate how tired someone is? I specifically refer to tiredness in the sense of sleepiness (as opposed to physical tiredness that might happen after a workout, for ...
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Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous? [migrated]

I have a project to write in Python that requires to write a function that given an ambiguous DNA (for example: KKGTACACCAG) sequence and a molecular weight interval, returns a list of all unambiguous ...
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1answer
73 views

How to align more than 2 sequences with Needleman-Wunsch?

I have a DNA sequence of a protein and around 1200 zinc finger target sequences. These zinc finger target sequences are 9 bp long, resulting in BLASTn not finding them in the sequence. Needleman-...
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1answer
57 views

Transcript without a start codon in mouse genome?

I am looking at the mouse reference genome in combination with ensemble annotation and am finding many transcripts that have no start codon. For example, the transcript ENSMUST00000193149 at position ...
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1answer
90 views

How can stat major get into bioinformatics?

I'm in my first semester of phd in information science and I want to work with bioinformatics professors. As a stat major, what should I prepare for before contacting some of them? I thought about ...
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1answer
60 views

Slightly different sequences returned by BLASTP

Probably this is very trivial but I am self-learning bioinformatics and I don't know who to ask for this kind of stuff. Also, apparently it is really hard to find information on general topics like ...
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37 views

Is it OK to use predicted protein sequences from RefSeq for protein sequence alignment?

I'm doing a project, and my goal is to do alignments of a particular gene product to see if there is any conservation of secondary structures across different species. So far, I have found a few from ...
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1answer
72 views

How to customize the output of my BLASTP output form

I'm trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with ...
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63 views

RNA-Seq: Is it conventional to use a threshold RPKM value to determine if a gene of interest is expressed in a sample?

I am interested in finding out at what stages of development a gene of interest is expressed in the human brain. I am using the Developmental Transcriptome tool from the Allen Brain Atlas to find this ...
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Is there a reference brain sample for the RNA-Seq data in the Developmental Transcriptome tool from the Allen Brain Atlas?

I am using the Developmental Transcriptome tool from the Allen Brain Atlas to determine at what stages of development a specific gene is expressed in the human brain. I have read the official ...
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Is there a newer/better book than Genome-Scale Algorithm Design available? It's from 2015

I'm considering buying the book "Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing" by Veli Mäkinnen and others. However, as this book was ...
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68 views

What reference genome was used to bootstrap the human genome?

As I understand it, when we map a genome, the process is much more complicated than say copying text out of a book. The genetic sequence cannot be copied from a genetic sample in a single pass, so ...
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1answer
97 views

What is a downstream target?

For example, in a systems biology analysis, what is a "downstream target" and why are these significant in pathway analyses? I have looked for answers on Google, DuckDuckGo, Wikipedia, etc. ...
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How to make Needleman-Wunch algorithm work if I restrict the number of gaps?

For example, I have two sequences (one is longer or equal to another) and I want to make a global alignment between them, but I only want to generate gaps in the shorter sequence. I see that the ...
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Difference between heritability on the scale of liability versus the scale of observation

I was reading a paper on disease heritability ("Estimating Missing Heritability for Disease from Genome-wide Association Studies") and it struck me that I don't have a great understanding of ...
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1answer
88 views

The Portion of the Earth's Biomass Attributable to Ants [duplicate]

An exterminator came to the house today (bad ant problem). He claimed that 20% of the earth's biomass is comprised of ants. I was surprised by this statement. I figured that I would post the question ...
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1answer
71 views

What is sigma factor PvdS?

I am using MEME suite tool for de novo motif discovery and when I use TomTom to compare my motifs with known motif database, I find that my genes could potentially be upregulated or downregulated by ...
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0answers
26 views

What's the process for determining whether a GC -> AT conversion in bisulfite sequencing is due to degradation?

I'm working on an ancient DNA project (humans) examining the methylation patterns for a single nuclear gene on chromosome 5. I understand the protocols of bisulfite sequencing, and in general how the ...
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1answer
83 views

What are the prospects in synthetic biology, especially in the introduction of biological computers? [closed]

One of the interesting areas of synthetic biology is the so-called biological computers. A biological computer refers to an engineered biological system that can perform computer-like operations. I ...
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28 views

genome wide identification of certain protein?

I'm trying to identify a set of enzymes (NALAAs) in a given bacterium, for which I have the WGS info. How do I shortlist candidate enzymes from my putative proteome? I tried using ScanProsite to ...
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1answer
46 views

Does gene isoform have different genetic location?

I would like to understand how a gene is assigned to a specific coordinate (e.g. NOC2L Chr1 879583(Start) 894679(End)). Next, let's say NOC2L gene has a few different isoforms, do those isoforms ...
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32 views

Differentiating molecules based on peptide sequence? How to annotate?

I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain ...
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65 views

What does does a blood sample tell you about an individual's identity?

I am working on a fiction/mystery scene where blood is found in a particular character's residence but the character themselves is missing. I would like to understand whether the law enforcement/...
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1answer
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Does anyone have a tutorial or some guide to get started with Rosetta protein modeling and design tool? (I am a Mac user) [closed]

I have been trying to get started with Rosetta protein modeling and design software bundle. I searched online but the tutorials in the Rosetta website are difficult follow. I have the binaries already ...
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Evidences supporting that coronavirus (SARS-CoV-2) came from bats

I was trying to find evidence that the coronavirus (SARS-CoV-2) came from bats. So far I know that coronavirus shared 96.2% overall genome sequence identity with a bat coronavirus RaTG13 from ...
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1answer
107 views

Get "DNA" of one parent based on its children [closed]

I'm no biology expert so bear with me, but I've been given a task to estimate alleles of an animal based on the animal's children and the children's other parents. I've looked up Mendel's laws but I'm ...
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1answer
50 views

Finding All of the Genes in a given Genome

I'm interested in finding the start position of each nucleotide in a given genome. I first went to EcoCyc and wrote a scraping script for their E coli data, but I can't find the same web page layout ...
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What are the advantages of long read sequencing for cancer oncogenomic research?

Currently I am using whole genome nanopore sequencing, Illumina short read and 10x linked read to study oncogenesis mechanisms of certain types of rare cancer. I am wondering about the advantages of ...
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129 views

Poly-G tails in NovaSeq Paired-end sequencing from museum samples

I'm currently working with DNA samples originating from museum specimens, this means they have been stored in formaldehyde for the last 50-100 years. The DNA I'm analysing has been sequenced by ...
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24 views

Why certain COGs appears more often in Humans Bacteria but not in plants Bacteria

I'm doing a Bioinformatic project from the university where I got a DB of COGS from Human & Plants Bacteria genomes and I need to find distinguishing sets in this DB and explain the biological ...
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1answer
40 views

Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?

I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is ...
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49 views

Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software

I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have ...
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Creating a phylogenetic tree from my selected publicly-available sequences (WGS) in NCBI

I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic ...
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1answer
40 views

Would there be more amino acid residues in the extracellular or intercellular space?

I am working on a bioinformatics project with HMMs and want to write some initiation probabilities for the location of amino acid residues. I know for different transmembrane proteins there will be ...
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1answer
133 views

How to identify an unknown species from a .fasta file containing its genome sequences [closed]

I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to ...
2
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1answer
75 views

DNA extraction kit for microbial mats, rocks, and soil in a remote area

I am hoping to perform a metagenomics study of samples from a lava tube. It will be in a remote area (with no large scientific equipment) and I would need to bring all scientific equipment myself. For ...
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0answers
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NCBI blast for exact match of short sequence

I'm trying to Blast for exact matches to the sequence: 'ATTGNNNNGCAAACCA' in the human transcriptome using NCBI Blast on its 'refseq_rna' database. However, when I do a basic query I get "No ...
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2answers
124 views

What exactly is "chromosome topology"?

I've been reading a lot about Hi-C lately, and this has been bothering me. So far as I can tell from reading around, the topology is related to the conformation of the linear chromosome. This seems ...
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1answer
54 views

Is there a negative correlation between the mRNA produced by the cell and the time of extraction? [closed]

I am doing some data analysis about gene expression time series. When I plot mRNA produced by P. Furiosus cells irradiated by gamma radiation against the time of extraction, it seems that there is a ...
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1answer
19 views

What is the best way to find which domains in a list of InterPro IDs are catalytic?

What is the best way to find which domains in a list of InterPro IDs are catalytic? (In this case, we are looking at human enzymes and their domains' InterPro IDs.) Thanks in advance! Setz
3
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1answer
78 views

Rigorous definition of the kinship coefficient and proof of a recursion thereof

I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...
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1answer
103 views

Why do doctors reccommend vegetable oils in high cholesterol and cardiovascular disease?

As there is high cholesterol in body why the patient need more fats and why the doctors are recommending it Transcribed: Vegetable oils are rich in polyunsaturated fatty acids (PUFA). The fatty acids ...
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1answer
63 views

Help Finding Specific BlaZ Gene Type Sequences on Genbank

I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that ...
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2answers
93 views

What is the energy required for storing and performing computations in synthetic computational biological cells?

I want to know the energy costs of various computations performed through synthetic biological circuits in terms of ATP. I am primarily interested in storing of bits, addition, and multiplication ...
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1answer
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Examining antibody - target interactions in PyMOL

I'm a student currently looking at antibody responses against a viral target protein of interest. I have my own, annotated PyMOL session of my protein and I also have .pdbs of crystallised antibody ...
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2answers
54 views

Metrics to analyze branch lengths in phylogenetic trees

I'm interested know about some basic metrics that could be used to discriminate trees based on their branch lengths. I know of branch length unaware topological/tree shape-based methods such as ...
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1answer
58 views

BLAST, using Smith-Waterman in the last step and S-score

In my bioinformatics course we studied the BLAST agorithm. After finding the HSP's and joining the HSPs together that are close enough and in a correct diagonal trend, we perform a next step: namely a ...
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1answer
29 views

What is multiplet nuclei capture rate?

I met this terminology in a publication.https://core.ac.uk/download/pdf/226940818.pdf. It's in the last sentence of the second paragraph in the text. I tried to search for it but didn't get a ...

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