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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112 views

How to calculate extent of Sequence similarity [closed]

I had a problem that I was wondering if it could be solved by one of the techniques/algorithms used in bioinformatics to give the extent of similarity. I have a Problem Statement: we have a sensor ...
4
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1answer
225 views

How does MEME compute the background frequency of nucleotides?

I am trying to calculate a log-odds matrix for MAST input, from a position-specific probability matrix for the motif in which I am interested. I would like to know how MEME estimates the background ...
4
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1answer
215 views

Software for counting fly eggs

Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid ...
4
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1answer
63 views

Parse PDB using DSR-PDB Library

I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose. I've encountered a problem. This library interprets CD1 atom of ILE ...
4
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1answer
92 views

Determining if a Protein Model Contains a Backbone Clash

I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be ...
4
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1answer
128 views

Epilepsy explained by computational neuroscience

A few years ago, on my maths masters, I did a module in theoretical neuroscience. I was shown that the mathematical framework the course developed for neurons, with a small adjustment in the ...
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2answers
85 views

Plotting metabolic networks?

I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes ...
4
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1answer
55 views

relative-rate of evolution

I am supposed to calculate the relative rate of evolution of two sequences (human and sheep) with a chicken serving as the outgroup. The sequences are pretty long, so I will just create a short ...
4
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2answers
87 views

Reference sequence for defining single nucleotide polymorphisms

Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in ("dbSNP—Database for Single ...
4
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1answer
49 views

Finding RNA Loops

I was rooting through the literature, but there is too much work on the topic of detecting loops in RNA and the RNA helices that go with them. Can anyone point to a good review on this topic or even ...
4
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1answer
161 views

What makes a DNA sequence motif a DNA sequence motif?

I've read about DNA sequence motifs, but still don't understand what makes some sequence a DNA sequence motif. Is this a well-defined concept? For, example, What are DNA sequence motifs? says: ...
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2answers
92 views

Combining gene expression data from two species

I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest ...
4
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1answer
95 views

Assembly of metagenomic data

I'm trying to assemble metagenomic data that comes from termite guts. The sequences comes from SOLiD and no paired, so the reads are extremely short (25bp). I have tried multiple assemblers (CLC, ...
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1answer
53 views

Where can I find histograms and tables of prevalence of mutations in cancer?

At some point in the past I found a cancer portal site which had aggregated data for the relationships between various mutations and their prevalence in cancer types and tumor data. The data was ...
4
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1answer
97 views

Online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology

Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology? I have tried the following: ...
4
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1answer
56 views

What value type would a chromosome position be in a database or form?

I wanted to create a tool for some fields like SIFT, Phenotype, etc..so for example I know Phenotype will have "Text" values or SIFT will have some determined values from a drop down list...but what ...
4
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1answer
47 views

Publicly available resources for learning metagenomics

We are starting a metagenomics project in our research group to study microbiota in the respiratory tract. Since the are no books yet about metagenomics, seems reading some reviews and online ...
4
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1answer
535 views

How do I view the simulated protein structure along with ligand in VMD?

I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot ...
4
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1answer
54 views

How to find ion/water channel related genes

We now have a collection of transcripts at hand. We would like to investigate some particular ones, which are ion/water channel related. How to perform this? Could anybody point out how to find the ...
4
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0answers
214 views

Statistical Coupling Analysis (SCA) to identify coevolved residues: use of ICA [closed]

We've begun to try out the SCA Matlab toolbox (latest version) downloaded from Dr. Rama Ranganathan's website, and, following the included tutorials, would like to apply it to our protein family. The ...
4
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0answers
83 views

At which step apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal)

I am trying to understand what is the best practice when preprocessing microarray data using a detection filter (on scanner p-value). Suppose I have a microarray dataset that I have to normalize with ...
4
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2answers
161 views

Biological key file format

I am in the process of creating biological key software tool for use on android devices. I would like to know if there are any established file formats for storing biological key data. Thanks
4
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0answers
110 views

Organize sequence database [closed]

I recently took up the task of organizing the sequencing database for a research project. I am still quite unsure of which database type I should use for this. Some advices/recommendations would be ...
3
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2answers
130 views

High sequence similarity but start codon isn't methionine

I have noticed in a particular genome sequence of a prokaryote that various regions in a sequence share similarity which is high(>80%) with known proteins. However, the start is not a methionine. Is ...
3
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3answers
316 views

Bioinformatics tool for “pairwise alignment” of complementary sequences?

I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate ...
3
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1answer
57 views

What information can Uniprot give me about phosphorylated forms of proteins?

I have a list of proteins formatted like this: ...
3
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1answer
432 views

Ka/Ks (dN/dS) analysis module for Python?

From this wiki article: In genetics, the Ka/Ks ratio (or ω, dN/dS), is the ratio of the number of Nonsynonymous substitutions per non-synonymous site (Ka) to the number of synonymous ...
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1answer
55 views

Is copy number variation dynamic?

Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need ...
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2answers
356 views

JMol “calculate HBONDS”: which atom is the donor/acceptor?

JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS". By outputting the state of the network, we can obtain a lisdt of H-bonds. Here's one line from an example ...
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1answer
704 views

What does phasing mean?

What does phasing mean in genetics/informatics? I've heard that a phased file is a file that has genes separated by chromosome, but can someone give a concrete definition of what phasing actually ...
3
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2answers
74 views

Microbiome Data

How is it possible to access microbiome data like that found here? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the Human Biome Project. Thanks for any ...
3
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1answer
105 views

What is the state-of-the-art algorithm for multiple sequence alignment?

Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment? How big is the need for better algorithms? How many sequences need to be alignment in a ...
3
votes
1answer
609 views

Difference between “transcriptional activity” and “RNA expression”

I am working with a network object where the nodes are different events in molecular biology. Specifically; Catalytic activity of X, RNA expression of X, GTP-bound activity of X, Kinase activity of ...
3
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1answer
118 views

Hamming distance between two DNA strings

By definition from Wikipedia, the Hamming distance between two strings of equal length is the number of positions at which the corresponding symbols are different. In other words, it is the number of ...
3
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2answers
141 views

How to use Autodock just for (re)scoring

I have some protein-ligand complexed that I have been docking with some other software and just want to use Autodock to evaluate those complexes. So, basically I just want to use it as a scoring ...
3
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1answer
81 views

Should the sum of RPKMs be constant over experiments

I have cufflinks data from 18 different RNA-seq experiments. I've noticed that if the sum all the RPKM values for a particular experiment, are vastly different between experiments. How could this be? ...
3
votes
1answer
209 views

The parameter for setting the number of mismatches in standalone blast

In a standalone blast search, is there a parameter that could be specified to fix the number of mismatches allowed in an alignment. I went through the parameters and I could only find parameters to ...
3
votes
1answer
727 views

RNA-seq analysis - q-values in cuffdiff

I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change ...
3
votes
1answer
126 views

Can compounds be predicted from Polyketide synthases gene clusters?

I've seen a few talks on the subject. From a gene cluster, there is some decent ability to determine which domains contribute to certain functional groups in the final metabolites. It sounds like this ...
3
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1answer
520 views

Displaying nucleotide at a single position from RNA-seq reads in a BAM file

How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am ...
3
votes
1answer
62 views

Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?

Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge ...
3
votes
1answer
36 views

SEREX serological analysis of cDNA expression library

What is Serological Analysis of cDNA expression library? I went through this article:http://cancerimmunity.org/serex/introduction/ but could not really make out. Can someone please explain this to me ...
3
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1answer
43 views

I2D vs STRING for protein-protein interactions

Can someone clearly explain me the differences between STRING and I2D(Interlogous interaction database) ? What does each database do best ? Which database is better for what kinds of studies etc ?
3
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1answer
51 views

PSI-BLAST website algorithm parameters

http://blast.ncbi.nlm.nih.gov/Blast.cgi In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? ...
3
votes
1answer
48 views

Regarding the NCBI FTP site

I am trying to extract information about SNP data from the FTP server of NCBI. Could someone please explain to me how the directory is organised? There are many many files and folders and I can't ...
3
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1answer
79 views

mFOLD prediction result interpretation

I am trying to predict the secondary structure of certain predicted pre-miRNAs through mFOLD which is the generally accepted technique for structure prediction in most studies. I am finding it hard to ...
3
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1answer
116 views

Biological meaning/interpretation of clustering coefficience

I have been looking for some time to find an answer to the following question. I would be grateful for any help/advice or directions. I work very frequently with large number of proteins and assess ...
3
votes
2answers
139 views

Why only heterogeneous SNVs for validation using genotyping arrays?

I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called ...
3
votes
1answer
84 views

What is a good source for info on disease frequency distribution among age groups?

I need information on the disease frequency distribution among age groups for an Android app I'm building... Hopefully I've come to the right place. Is there a good data source for this? Like a ...
3
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1answer
97 views

Superposing DNA

I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used. I can ...