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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179 views

explanation of meaning of high-throughput

Almost all of the papers about bioinformatics, I faced with the high-throughput word, but I could not find any explanation about it (I think it is so easy to understand and thats why anyone explains ...
4
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2answers
296 views

How can I text-mine full-text articles from PubMed? [closed]

I want to do a text mining study using full-text versions of articles I find on PubMed. My intended search protocol will be roughly as follows: Search PubMed using a gene name (and any alternate ...
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2answers
52 views

where to find the relative frequency distribution of synonymous codons

Most amino acids can be encoded by more than one codon. For example, Serine can be encoded by any one of ...
4
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2answers
137 views

positive and negative feedback

I want to know more about positive feedback in gene regulation and to know the similarity and differences between positive and negative feedbacks.
4
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2answers
174 views

How can I fetch nucleotide sequences based on ENA accession numbers and positions?

I have a list of ENA accession numbers and a start and end position in each sequence. In the end I want to align all those sequences, but first I have to fetch them and the list is too long to do that ...
4
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1answer
114 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
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4answers
298 views

Is there a PSI-BLAST for nucleotide sequences?

I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs ...
4
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1answer
155 views

What is benjamini

I was doing some gene expression analysis using this tool http://david.abcc.ncifcrf.gov/summary.jsp. However, I have a confusion about what benjamini is. I fed it some gene list and it gave me some ...
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63 views

Main methods used to predict functional annotations in GO

Can someone provide me some information about the main method used to predict the inferred electronic annotations in Gene Ontology?
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4answers
2k views

E-value BLAST cut-off

What is the best cut-off for e-value in BLAST? Some say 0.01 ,others 0.0001? Even BLAST tutorials don't give a very clear idea about which cutoff suits which purpose? Could some experts give me a ...
4
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1answer
61 views

Where to find E.coli gene expression data?

I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc. I have ...
4
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1answer
73 views

Nomenclature of genes and proteins

With respect to this paper: Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen In the abstract, I found names such as Rab6 and Vps35 and TNPO3. So Rab6 ...
4
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2answers
166 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 ...
4
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2answers
432 views

Could be an union/synergy between Math, Computer Science and Marine Biology?

I'm studing for my bachelor's degree in Natural Science and I have to chose the path for my future life. I have to chose the right kind of graduate studies. Since I love computer science, maths and ...
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4answers
1k views

Multiple sequence alignment - how to align everything to 1 gene sequence?

I'm having trouble aligning 3 sequences together - the total gene (~2500bp) and the forward and reverse sequences that are ~1000bp in length. Now I'm using Clustal X2, but the problem is that the ...
4
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1answer
66 views

Visualising a subset of the tree of life

I understand that many curated trees of life already exist (eg http://tolweb.org/tree/) but is there any website that allows one to input a list of organisms, and then produce the current best guess ...
4
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1answer
114 views

Blosum matrix with probabilities instead of the positive and negative scores

I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like ...
4
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1answer
294 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 ...
4
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2answers
138 views

GO terms for non-model organisms

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have ...
4
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1answer
1k views

What does conditional analysis of a SNP in a GWA study entail?

I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
4
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2answers
201 views

Confusion related to gene expression

I have a set of gene expression data downloaded from http://www.ncbi.nlm.nih.gov/geo. I have two sets of data, one is the raw probe intensity data set in the form of CEL files. Another is processed ...
4
votes
1answer
47 views

Multistability in the lactose ultization network

Reading the paper here, I'm confused about the production of figure 4d. The method of production is detailed in the supplementary information under the heading "Theoretical phase diagram". ...
4
votes
1answer
50 views

RNA-seq Data on domestic animal with different environment

I want to find the RNAseq data available on domestic animals in different environments. If microarray data is available, it would be more useful. If you know I would appreciate to inform me.
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4answers
118 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
259 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
votes
1answer
273 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
69 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
136 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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1answer
27 views

Epistasis Across Chromosomes and Individuals 'Homozygous for Interactions'

Apologies for any failures in nomenclature. I'm a mathematician who is making a foray into genetics for a masters thesis. Specifically, I'm generating artificial diploid genetic sequence data and ...
4
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2answers
67 views

Relative microRNA comparison from from TCGA data?

I have a conceptual question that I was hoping someone could answer. Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after ...
4
votes
1answer
79 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?
4
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2answers
128 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
168 views

Local storage of NCBI database in MongoDB [closed]

My short term goal in a project is to build a local database of the NCBI dbSNP database. The data and schema are available on the FTP site(). I was going to implement the database using MySQL, but I ...
4
votes
1answer
64 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
107 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
51 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
votes
1answer
188 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: ...
4
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2answers
97 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
votes
1answer
97 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, ...
4
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1answer
54 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
votes
1answer
109 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
votes
1answer
58 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
71 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
votes
1answer
69 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 ...
4
votes
1answer
703 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
votes
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
261 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
votes
2answers
177 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
votes
0answers
121 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
142 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 ...