Bioinformatics connects life sciences and quantitative sciences, typically involving the application of software and algorithms to solve computationally intensive questions, such as those in genomics, sequence analysis, and systems biology. Questions tagged Bioinformatics should have a direct ...

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How to learn DNA Origami

Can you tell me is there any good softwares and tutorials which can be used to learn DNA Origami. I am new to this and want to learn from basics. Advance thanks for your help edited: INSILICO
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How to get only perfect matches with blastn?

I have installed Blast locally and I've configured the nucleotide database to use. I want to search some sequences (from a .fastafile) in this genome. So I used blastn: ...
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26 views

Finding confidence level of miRNA disease associations

I'm an undergraduate computer engineering student, and I have a project about bioinformatics. In this manner, I need to find prediction( or association I'm not sure the correct terminology) confidence ...
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48 views

How do I identify the protein with the highest Disulfide bond density? i.e protein with highest ratio of Disulphide bonds per Peptide bond? [closed]

I want to list all proteins in the protein database and list them by the ratio of number of disulphide bonds per peptide bond. I am not particular about the reliability of identification of ...
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2answers
66 views

Do variant callers miss rare variants in reference?

Generally variant calling programs (such as GATK-UnifiedGenotyper) look for differences between reference genome and submitted sequence. However, we all know that reference genome consist rare ...
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1answer
102 views

what the best E-value cutoff in the miRNA homology search

I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop ...
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52 views

Biology Experiment Data (Hodgkin-Huxley)

I'm doing research into the Hodgkin-Huxley Model from an electronics/mathematics perspective and I'm looking to find actual numerical results from experiments on squid axons. I want to compare the ...
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32 views

Genome-wide methylation analysis: sources of technical error?

We are doing a genome-wide analysis of methylation via bisulfite sequencing for an insect species. Previous experimental techniques have suggested the presence of methylation in this organism, ...
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22 views

How are HSPs identified in UCLUST

I am new in Bioinformatics and recently studying UCLUST algorithm by Robert Edgar(2010). It is a fast sequence searching and clustering algorithm. The algorithm is heuristic based. I studied that ...
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54 views

Can a heterozygous allele show non-heterozygous expression in a family?

I'm doing a family study looking for novel cancer-associated variants in germ-line samples; the goal is to find candidate biomarkers which might be used for early detection. At an earlier step our ...
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162 views

Software to calculate Fst from sequence data

I'm looking for a software to calculate Fst from 3 loci DNA data of individuals from a metapopulation. I don't have any prior on the population structure (have no idea of the number of subpopulations ...
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39 views

dbSNP database table desciptions

I am trying to build a local implementation of dbSNP. I would like to know the descriptions of tables listed on ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606 and on ...
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45 views

Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?

E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms ...
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230 views

ChIP-seq and the output of SPP

I have been processing some ChIP-seq data with the R package spp. I looked through the literature (ENCODE uses it) and it seemed that spp is indicated as a good program to use. I have found and ...
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168 views

Too few transcripts from transcriptome assembler Oases

I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks. Here is my running command: ...
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304 views

Turn off multithreading in pymol [closed]

By default, pymol seems to grab the number of cores on the system for rendering. How can I force it to only use one core? Motivation: I have a large collection ...
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551 views

What is the difference between second and third generation sequencing

I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to ...
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445 views

basic programming and bioinformatics [closed]

As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work ...
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2answers
59 views

Trying to understand the big picture behind DNA sequencing, alignment and searching

I'm about to start a bioinformatics research project but I haven't any biological background. I know my project is in regards to a performance analysis of DNA sequencing and searching "weapons" like ...
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1answer
95 views

Generating custom human DNA sequences based on traits such as eye colour?

I'm wondering if it would be possible to create software (unless some already exists, but I couldn't find any) to generate human DNA (the base pairs on the double helix) containing genes representing ...
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1answer
131 views

Plastid and mitochondria

I am not biologist, so please bear with me for this basic question. Although I tried googling, I am confused. What is difference between plastid, chloroplast and mitochondria? Are there any plant ...
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2answers
95 views

What kind of technology is required for plant seed DNA printing? [closed]

I'm a programmer so I have little knowledge in the field of biology. However I have an interest in plants, GMOs and DNA (in terms of programming). So, I want to know what kind of technology is ...
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1answer
58 views

How can I download a gene sequence from GenBank (NCBI)? [closed]

Could you tell me the steps to find and download a gene sequence from GeneBank? I would appreciate your help.
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2answers
119 views

Gene perturbation, what is it used for, explain to computer scientists? [closed]

I am trying to build a gene regulation network, and I need some basic knowledge of it. So, in gene research, we perturb genes. Such as knock down them? Can people tell 2 or 3 experiment methods to ...
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62 views

Which types of hydrogen bonds are known to exist in RNA secondary structures?

I'm programming an implementation of an algorithm for pattern matching in RNA structures. The algorithm assumes the following types of base pairs: Plain: No base pairs (just the primary structure of ...
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1answer
89 views

Transcribing DNA to mRNA with introns

I have a problem in my bioinformatics class that I thought I was doing right, but someone else is getting a different answer. Here is the problem: Given the following DNA sequence, ...
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1answer
67 views

Is there a way to see what representations are currently displayed in PyMOL?

I am using PyMol to visualize .pdb protein structures. I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot ...
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1answer
44 views

What are pseudoknots?

I'm trying to get my head around what a pseudoknot is and how I can identify them given some RNA string. For example, suppose I have a string s = CGUUGUGUACACGAUAGUACAU. Suppose the two longest ...
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2answers
83 views

Recommended sequence clustering algorithm for transcriptome data

I'm working on a project where I'm going to analyze a large amount of transcriptome data. After assembling our RNA-Seq reads into contigs using Trinity, it looks like I'm going to have about 10GB of ...
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2answers
286 views

Draw simplified phylogenetic tree for kids

I need to draw simple, phylogenetic tree for kids lecture. I am looking for an online tool where I can enter organisms (e.g., human, wasp, fungus) and get figure of a phylogenetic tree. Tree should ...
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2answers
138 views

What is most simple eukaryotic genome?

Expressed in number of Base Pairs or Bytes, about how large is the simplest eukaryotic genome? How much of this is 'junk-DNA' (non-coding)?
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39 views

Single channel micro arrays

What does single channel microarray mean? When is it used? Thank you for your case in advance.
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3answers
104 views

Are there tools for automatically parsing glycan names into tree structures?

My colleague and I are working on a project involving data produced at a glycan microarray facility. The array data that came back to us were a list of glycan names (in IUPAC condensed format). We ...
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3answers
69 views

Using PSI-BLAST

I understand that the first BLAST yields almost the same results as blastp. The second time the iterated blast generates different results as it uses different matrix based on our first result. But I ...
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1answer
199 views

Codon alignment via Python? [closed]

I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process. So far.. I retrive pairs of orthologous DNA sequences from ...
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2answers
97 views

what does sequences overlap indicate

what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other and how does one go on to ...
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1answer
135 views

Chemical structure prediction

I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but are there any programs which will go from formula to structure ...
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1answer
38 views

An example for N50? Why do we need it?

I'm trying to understand N50 on the wikipedia. But I was unable to get a sense of the definition: Given a set of contigs, each with its own length, the N50 length is defined as the length for ...
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1answer
62 views

What is the difference between gene and CDS annotations?

I have a bunch of sequence files fetched from the EBI ENA and I'm trying to find the end of the 5' UTR for specific genes. The UTR itself doesn't seem to be annotated in most sequence files I have. ...
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2answers
69 views

Aligning multiple sequences in heterogeneous group

I have a list of ~200 DNA sequences, representing probably 50 different genomic regions but they're all mixed up. For example, if I have seq1, seq2.... seq10, ...
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1answer
62 views

Modeling intracellular interactions between sender and receiver bacteria

I am involved in a modelling task of a biological process described as follows: -- "Objective: to model behavior of a sender receiver type system The process goes as follows Pre-signal [PS] is in ...
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1answer
133 views

Distance matrix with different length sequences

In a project we're doing (in python), we want to create a distance matrix for a phylogenetic tree with multiple, different length sequences. However, what we've seen so far (AlignIO in biopython, ...
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1answer
31 views

PDB file SEQRES have different datas?

In PDB file, SEQRES represent the aminoacids but some pdb file present the "GLC" and some other. for example ...
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1answer
111 views

Datasets of aligned nucleotide sequences [closed]

Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there? (I would like to use such datasets for training the alignment ...
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1answer
52 views

How to selectively download 3 fields from every record in UniProtKB?

I want to download a comprehensive table of protein names from uniprot.org. More precisely, I want to generate a tab-delimited table consisting of the id ...
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1answer
66 views

To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)

I have to answer a question about a sub-task of my thesis: Can the bacteria X produce the protein Y? I searched of course Google and BLAST. There is no data supporting that this specific bacteria ...
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2answers
350 views

How do download a list of the gene length of all genes?

I would like to get the gene length information of all the human genes. Is there a quick way to get this information? Thank you!
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1answer
60 views

Genome Assembly Using Reads

I'm taking an online bioinformatics class and I am stuck on a problem. The resources I have found don't help that much. Here is the problem: "Assemble the error-free reads from a circular genome on ...
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2answers
167 views

How do you find pre-miRNAs from mature miRNA Blast output?

So in short, I did a blastn with standalone blast using all known miRNAs against the EST sequences in a genome (word length 7 and e-value 0.01). Now to confirm one of the next steps would be obtain ...
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1answer
280 views

What are the differences between HPRD and BIOGRID databases?

What are the differences between HPRD and BIOGRID protein-protein interactions databases? What are their purposes? Why do we need two different databases? How is data collected into each one? How ...