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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Accuracy of genome size estimation by flow cytometry

I'm working on a genome project and using an in silico k-mer analysis to estimate the size of our genome based on the available Illumina reads. The k-mer based estimate is consistent across a wide ...
3
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1answer
53 views

Statistics on energy consumption breakdown per biological functions across organisms?

Are there any statistics available on how much energy organisms use for each biological functions (i.e. something similar to the line of "Bacteria spend X% of energy on information processing, Y% for ...
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3answers
92 views

fastq-dump using mkfifo to stream data

So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk. I'm curious whether ...
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2answers
94 views

Consensus codon optimization by organism

Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables ...
2
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1answer
81 views

Bowtie: cannot read fasta file?

I am trying to use bowtie2 to analyze my data in FASTA format, but it seems that this version can't read properly my data. My command line is as follows: ...
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2answers
45 views

Simulating Drug Entry in Protein and binding?

Is there any simulation protocol or paper which can simulate the dynamics of drug entry and interaction with the target protein?
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1answer
304 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 ...
2
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2answers
66 views

peptide MHC microarray

"The recent technology is peptide–MHC microarray or artificial antigen-presenting chip. In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a ...
2
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2answers
40 views

RNA secondary structure comparison

Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common ...
2
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1answer
113 views

Expanding the SETI initiative to seek intelligent data within DNA sequences?

I've recently read a couple articles dealing with long term data storage, and DNA was suggested as one of the prime candidates for long term storage of digital data additionally, there is this article ...
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1answer
82 views

How to build S16 rRNAs phylogenetic trees?

Here is what I know so far: Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al.[1] it is enough to select the most similar ones. There are stem regions in the ...
2
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1answer
183 views

MOL2 to PDBQT conversion via OpenBabel and MGLTools removes hydrogen atoms

I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms ...
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3answers
1k views

Primer design for Gibson assembly

I'm trying to design a primer for Gibson assembly. My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid. I am unsure how to design my primers for ...
2
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1answer
41 views

Data Bias in protein-protein interactions data

Databases like STRING have so many predicted as well as experimental interactions data for many organisms.However there is a bias in the data which they have?. a)The first is gene co-occurrence ...
2
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1answer
74 views

What do the Clustal Alignment Symbols Mean?

Occasionally I will run protein alignments on peptide families and I can never remember what the symbols mean to show degrees of identity. What do they mean?
2
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1answer
50 views

H O N C alternatives for organic life?

Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures. Are there ...
2
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2answers
91 views

chimeric sequences [closed]

I understand that chimeric sequence identification is done in results of sequencing projects to remove them and improve the quality of the output. I am unsure as to how they show up during sequencing. ...
2
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1answer
44 views

Number of autoregulation and FFL motifs in a network

Suppose we have a network with N* nodes (N* is the number of internal nodes). Every directed link in this network exists with probability p. What would be the number of: motifs that are ...
2
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2answers
56 views

Connection between genes and pathways

I am reading about a paper about inferencing pathway information in cancer cells. Authors refer to ERBB2 as a gene and a pathway. I don't have solid biology background. What exactly means when we ...
2
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1answer
443 views

What do rs id, allele coded 0 and allele coded 1 mean?

So, for a project I've been working on (different story), I've been looking at the HapMap Project, and their free online files. In their README file, they talk about how for each legend file for each ...
2
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3answers
113 views

What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?

I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
2
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1answer
89 views

Confusion related to a term probe-by-background interaction

I was reading a paper related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, ...
2
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1answer
185 views

One flybase gene number (FBgn), many Affymetrix Id's

I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the Flybase file required to do so (as ...
2
votes
1answer
134 views

How to determine the direction of regulation of a gene by comparing gene expressions?

I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a ...
2
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1answer
24 views

Gene Sequencing and Plasmapper

Is there anything similar to this in Java (especially the circular map sequencing along with hover effect)? For information I would like to convey that I am using Plasmapper and BioJava for achieving ...
2
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1answer
57 views

Difference between sequential and conformational epitope

Is the difference only in its structure? Like conformational epitope has 3D structure while sequential has a linear structure?(I have not studied biology since last 8 years and now I am going through ...
2
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2answers
86 views

How do I perform recurring pattern mining or regular expressions of nucleotide sequences?

I am interested in performing nucleotide sequence pattern-mining (regular expressions) which is 12 characters (sequences) in length from a dataset. Is that possible to script using MATLAB?
2
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1answer
128 views

Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions

I am working with RNA-seq data from the Cancer Genome Atlas TCGA and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk ...
2
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2answers
47 views

Hiding identical sequences in NCBI web interface

Sometimes there are identical sequences in Genbank/Genpept, most often coming from the same species but different strains. Ie if I look up "bacteria chitin synthase", the 624-aa protein from Dickeya ...
2
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2answers
81 views

Sequence alignment scoring

The following table is from Deonier's text Computational Gene Analysis at p. 152. This is an exercise in global sequence alignment and scoring of alternative sequences. The text proposed a solution ...
2
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2answers
61 views

Bioinformatics : Drawbacks of using ORA(Overlap Analysis)

What do you think are the potential drawbacks/weakness of using ORA to explain distinction between two phenotypes. I identified a few which were the dependencies of DE and the statistical method used ...
2
votes
1answer
132 views

Any tool to align whole genome sequence data to another genome and give exon regions a higher mark?

I want to align WGS data from several mammals to one reference such as the human genome sequence. Since in most cases exons should be conserved and spliced in the same way and introns should vary, I ...
2
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1answer
200 views

How do PLINK files and HapMap Phased files differ?

I know that PLINK and HapMap files show the same information, but can you give a thorough explanation of how exactly they differ.
2
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1answer
53 views

How can I view modENCODE data faster?

I am trying to view several data tracks in the modENCODE GBrowse genomic browser. However, the site is so slow, it is practically unworkable. Is there a faster way to explore the data?
2
votes
1answer
740 views

Problems with analysis of small RNAseq data - Adapter trimming

I have always faced a problem while analyzing small RNAseq data, at the step of adapter trimming. Overview of small RNAseq (Illumina) RNA is size fractionated using columns or PAGE 3' and 5' ...
2
votes
1answer
51 views

Confusion related to the DAVID tool

I am trying to use the DAVID tool to do some gene analysis. I have some probe set intensities for some cancer cell lines. I found this link in the DAVID tool http://david.abcc.ncifcrf.gov/tools.jsp. I ...
2
votes
1answer
114 views

How can I compare rates of evolution for two sets of proteins?

I have a list of candidate proteins as the result of my analysis. I am now trying to find various characteristics that they have in common. One of the things I would like to check is if my candidates ...
2
votes
1answer
22 views

Is it possible to dock multiple ligands with the target?

Is it possible to dock multiple ligands with a target? If so, what is the suitable software used for? -- Is it possible to fix specific docking region for the target (or) automatic?
2
votes
1answer
37 views

Sequencing a specific region of a genome

First off, I'm new to bioinformatics and I am learning about DNA sequencing. Let's say that I knew that a specific region of a genome which contained information about a disease (whether it a person ...
2
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1answer
59 views

Heterozygosity and the Wright-Fisher model

I was reading the textbook Probability Models for DNA Sequence Evolution by Durrett. In chapter 1, he discusses the Wright Fisher model and the coalescent theory ...
2
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1answer
40 views

Quantitative Comparisons of Phylogenetic trees

I am working on a broad phylogenomic analysis of proteins involved in one particular cellular process. I have constructed a phylogenetic tree for each protein. I am now working on comparing those ...
2
votes
1answer
78 views

Steps to confirm if predicted miRNA is good or bad

I aligned all miRNAs available to the supercontigs of a particular genome with certain parameters (e value of 0.01 and a word match of atleast 7 as suggested in this paper). I have also isolated the ...
2
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1answer
54 views

Converting Ensembl Compara gene tree DNA alignment to corresponding amino acid alignment

I have Ensembl compara gene tree alignments (Compara.gene_trees.57.fasta.gz downloaded from ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/) in nucleotide format. According to ...
2
votes
1answer
57 views

Comparing Shine Dalgarno scores, creating a distribution

I am in the process of creating a poster for the phage that I recently annotated. The phage is an A4 and the portion of the poster I am working on is analyzing the data that we have collected. I have ...
2
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2answers
73 views

Databases for metabolic pathways of human disease

Which databases contain the metabolic pathway of human diseases? I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.
2
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1answer
323 views

How to check if a fastq file has single or paired end reads

I am trying to check if a fastq file has single or paired end reads. How can I achieve this with an error-proof method? I checked wikipedia and MAQ but I want to know if is there a reliable document ...
2
votes
1answer
104 views

Transition/Transversion ratio

I'm taking a bioinformatics class and at this point we are just going over basic stuff about molecular biology. Half of the class is doing reading/research on our own, so there isn't much class time ...
2
votes
1answer
59 views

Mass Spectrometry Terminology

I began reading this paper (http://www.biomedcentral.com/1471-2105/14/56) and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere. Consider the following ...
2
votes
2answers
119 views

Image analysis of GFP-tagged protein localization bursts

I'm reading an article (full text here) that analyze the dynamics of localization of a GFP-tagged transcription factor (Crz1) over the time at the single-cell level, by taking movies in a fluorescent ...
2
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1answer
63 views

Is the book “Bioinformatics for Geneticists” outdated?

I am going to be working with genetics data in my organization's data warehouse next year and helping our biotechnology department. I work in academic research, but I have very little genomics ...