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 find gene variation in NCBI?

I am looking for variations of my gene so that I can design a primer. But, I do not know how to found the relative links in NCBI. Where can I start?
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113 views

How to use swiss-mod to predict the secondary structure and 3D structure of a protein?

I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling. I'm getting confused with how and when to use Jpred, swiss-mod, ...
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2answers
301 views

GATK workflow for Cancer

I am just starting to learn to use bioinformatics tools. My university has a limited and expensive bioinformatics team, so I'm mostly on my own except for big questions. I am planning to use GATK to ...
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1answer
190 views

How to perform a DNA structural alignment in pymol

How can I "fit" two DNA structures having different nucleotide sequences in pymol? I would like to use the structure of a DNA binding protein in pdb (1h9t), which is bound to DNA in the pdb file, ...
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242 views

Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

I experience big discrepancies when calculating melting temperature of RNA 7-mers with Biopython over values generated by a popular algorithm. I tried the nearest neighbour algorithm with RNA and ...
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45 views

Running (standalone) PSI-BLAST Against Multiple Queries

I'm new in standalone blast+ and in linux terminal. I set the bash-profile to load the PATH and BLASTDB for my blast already, but I don't know how to use psi-blast yet. How can I do the search ...
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1answer
642 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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3answers
43 views

importance of cDNA sequencing of a specific gene in different plants

i want to know what if i made a sequence of cDNA of a specific gene in different plants - what is the important from the sequence and can if found difference between plants , and can i use this ...
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32 views

Biological modeling languages - some basic issues

I am trying to get used to with couple of modeling languages in biological context like SBML, BioPAX, Kappa and BEL. Some basic issues came up to my mind that are unclear to me even after a lot of ...
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1answer
102 views

How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis

I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be ...
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1answer
48 views

In DNA sequencing, is “mate pairs” synonymous with “paired ends”? If not, how do they differ?

By just looking at Roach et al's paper I get the impression that they are the same thing, and the Wikipedia URL for the former is a redirect to the latter. However, I suspect they are not exactly the ...
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2answers
48 views

How does one find the corresponding SNPs in the pair of chromonosmes in a FASTA file?

You might say I'm an amateur bioinformatician, or trying to become one. I have a BAM file, from which I have succeeded, using UGENE , in extracting consensus data in FASTA format. I now see a single ...
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637 views

Are there examples of encryption in nature?

There are examples of mathematics in nature such as Fibonacci number, fractals, etc. Are there examples of encrypted information? What I am looking for is a pattern that seems random on the ...
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1answer
34 views

Metrics or operations on genome sequences in human genomic research?

Edit distance may be an important metric for measuring the similarity of two genome sequences. For example, if A = GCAATT and B= CGAATA, then the edit distance of A and B is 3. Such a metric is ...
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1answer
50 views

How to Determine the Most Conserved Sequence from BLAST Result?

I used BLAST to find the best aligned DNA sequence to my query sequence. The BLAST result shows a number of sequences that it calculated to be the best aligned sequences to the query sequence that I ...
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1answer
61 views

How to annotate a .broadpeak file with 9 columns?

I have this peak file I retrieved from an ENCODE chip-seq matrix. Its .broadpeak file looks like this: ...
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1answer
64 views

Does a DNA sequence has its own derivation tree or pattern?

I am new to bioinformatics and natural language processing. In linguistics, they have Treebank - derivation/parse tree for each sentence. For example, a sentence "Sara sleeps" can be visualized by a ...
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2answers
116 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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2answers
700 views

List of np-hard problems in biology/bioinformatics

I'm not sure if this is the right place for this but... I am looking for a list of computationally "hard" problems such that if a problem from this list could be solved effectively, it would be ...
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2answers
60 views

yeast protein secondary structure

i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous ...
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1answer
173 views

How does one calculate the amount of oxygen produced by trees?

I'm currently working on a project to measure the impact of tree planting. Calculating the amount of oxygen seems harder than I imagined. Of-course there's the type and size of the tree and the ...
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1answer
92 views

difference in genetic instuctions between male and female [duplicate]

I'm a computer science graduate so please bear with me the following computer program : mov ecx, -1 INC ecx consist of 2 instructions (mov,inc) each working on specific data , can genetics ...
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2answers
39 views

Data Retrival from the GenBank?

When I go to NCBI & Select nucleotide option there and in search box write For Example CNGA3 gene the page shows that there are 553 items.I know the method of downloading or retrieving the One ...
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1answer
47 views

What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way?

First post here, so bare with me if I violate any etiquette or formatting rules. Let's say I've got a protein in humans. When it interacts with an ncRNA found in humans, it does something that I'm ...
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117 views

Are there any de-novo genome assembly programs for HADOOP?

I have access to a small (approx 20 nodes) cluster that has HADOOP running on it, and I need to do some de-novo genome assembly. I'd like to ask is anyone knows of any program that can do this on a ...
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0answers
60 views

How do you create a .snp datafile?

I'm looking to use the software DIYABC 2.1.0 to apply approximate bayesian computing (ABC) to some resequenced data that I have. The resequenced data is in FASTA format however, and the software ...
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27 views

Batch several sequences for absent restriction sites

I have a collection of about 120 7kB sequences I would like to check for ether a list of specific restriction sites, or what restriction sites might be absent in all of them. Is there a app or ...
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1answer
57 views

How to predict a mRNA secondary structure with a large sequence?

When I use some web servers to predict a mRNA secondary structure, I find they always required in a small size sequence. If I use a long sequence and cut it into small parts, do these small parts ...
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3answers
559 views

What is the biological significance of finding palindromes in DNA sequence?

I found a function called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of ...
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2answers
142 views

Is there a database of cell images?

We're working on an algorithm for processing images of cells, similar to but much more basic than Cell Profiler, and we are looking for a large database of cell images to test our software. Can anyone ...
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1answer
35 views

Why my base-quality in alignment is not perfect?

I have a fasta file with some DNA sequences. I would like to simulate next-generation sequencing reads from it. I'm doing it without any base error and mutation error. ...
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0answers
39 views

Shortest path and influenza spread

I have been researching on the applications of the shortest path problem to biology. I thought about modelling the spread of influenza virus and wondering if there was previous research on the topic. ...
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0answers
25 views

NCBI EUtils. Get Homolog infromation using Gene ID

How to retrieve homologs information in xml or json format from NCBI using gene ID? I tried one URL: ...
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1answer
13 views

num_tol_term in PeptideProphet result

What is the meaning of the num_tol_term attribute in a PeptideProphet (pep.xml) search_hit? ...
2
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1answer
81 views

What is biological intuition?

Whenever I read or learn about prediction tools or aligners or motif detectors, I also hear that they are lacking in something called biological intuition. But I haven't been able to find a solid ...
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134 views

Do the bacterial species X, Y, Z code for proteins A, B, C?

My PI has assigned me a task to gather evidence to determine whether or not a list of particular species of Campylobacter and Helicobacter code for a list of several proteins. To put it simply I’ve ...
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0answers
41 views

What program was used to create this visualization of a neighbor-joining tree?

I know there are many programs out there to visualize neighbor-joining trees in phylogenetics. I have a tree in Newick format. Does anyone recognize the features of this image as coming from a ...
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0answers
73 views

How to identify a pseudogene to a specific protein coding genes?

Pseudogenes are those sequences in the genome that bear similarity to specific protein coding genes, but nevertheless are unable to produce functional proteins due to existence of frameshifts, prema- ...
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1answer
102 views

How to find a Cancer PPI network data [closed]

I need a Protein Protein Interactions network of Cancer (any type - just I want a PPI of any type cancer), I search and see DIP PPI and .... How to specify that is Cancer PPI and how to get a PPI of ...
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2answers
1k views

Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
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3answers
2k views

120-year-old gene regulation problem independently solved by a computer. How?

My Background: I'm a mathematics graduate student with a physics background. I have a very little biology knowledge and a little knowledge of machine learning and statistics. Topic: I recently ...
3
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1answer
99 views

Why perform imputation?

Genetics datasets contain measurements for millions of single nucleotide polymorphisms (SNPs). Some (usually small) percentage of these values are of low confidence, and are labeled as missing values. ...
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1answer
70 views

How to interpret the simple sequence repeat (SSR) on the coding sequence, but not the related protein sequence?

I have predicted some SSR repeat on the gene of interest using SSRLocator program, which the result creates a question for me. Please consider the below sequence, which is part of gene sequence of ...
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0answers
67 views

How to characterise a protein family in a putative genome island?

We have sequenced the genome of 200 bacterial strains belonging to the same species, a swine bacterial pathogen. In a previous work, it was observed that a protein family of adhesins is present in ...
3
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1answer
54 views

blastn: What substitution matrix is used?

I'm currently working aligning sequences, and I need to compute similarity between pairs of DNA 'words' of a particular length. For amino acids I am able to use the substitution matrices in Biopython ...
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2answers
57 views

How can I find some pieces of the genome of a microorganism?

I have figured out how to download the fasta of the genomes of microorganisms, for example the botulism bacteria and the spirulina algae. However, I want to find a fasta file for some significant ...
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1answer
147 views

Normalised gene counts to edgeR/DESeq2?

Both very popular differential expression packages assume a raw gene matrix count. This makes sense because the statistical model models the library depth. But what if I normalize my counts with say, ...
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1answer
61 views

Is studying complete mitochondrial genome need biological lab work?

The research complete mitochondrial genome study done on species: Juema pig Sus scrofa (Suina: Suidae) from southern Gansu red rainbowfish speckled dace, Rhinichthys osculus white char Salvelinus ...
3
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1answer
146 views

What is the last heavy atom of an amino acid?

I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it ...
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2answers
89 views

It's right to say coding sequence is part of exon sequence?

Some basic ambiguities making me confused. I downloaded 5'UTR, CDS, 3'UTR, and exon sequences, separately from Biomart for a gene P4HA2 (Homo sapiens) and found some simple sequence repeat (SSR) on ...