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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301 views

Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. The ssm is in the following format: ...
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1answer
195 views

How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median

I want to transform a TCGA mRNA expression matrix (in linear data format) to log2-ratios and then run a feature (gene) selection, selecting the 1000 most variant genes (genes with higher standard ...
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2answers
247 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 ...
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2answers
990 views

TCGA gene expression data are missing matched normal

I'm trying to use the TCGA data portal to get gene expression data for cancer tissues, but I'm not sure what "Tumor matched normal" means. It is unclear to me if the values are already compared to a ...
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2answers
537 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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0answers
49 views

Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
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1answer
100 views

What makes a good phylogenetic tree?

How can one improve a phylogenetic tree? If one was to make the 'golden standard' of phylogenetic trees what features would it have? Would it be highly reliable, well resolved etc? What other features ...
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0answers
51 views

Best software for protein in electric field modeling?

I'm trying to find a free, or cheap, software program to model the movement of a heterotrimeric protein in an alternating electric field. The dipole and crystal structure of the trimer are known. ...
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1answer
156 views
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45 views

Common Metrics of Assessing DNA Sequence Quality

What are commonly accepted metrics for assessing DNA sequence quality (platform-specific answers are fine)? I am relatively new to this topic, and I want to either find or code (in Python or C++) ...
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60 views

Compare Proteins - Structural / Sequence parameters [closed]

I have been working on algorithms that extract co evolutionary signatures from protein sequence. As a result of my work I got some evolutionary information which possibly explains cotranslational ...
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31 views
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2answers
112 views

Core Biological concepts explained to a Computer Scientist?

I am a computer scientist delving into Bioinformatics and I need to gain insight in biological phenomena. How would you explain three core concepts as: Evolution, Selection and Variation, to a ...
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1answer
144 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 ...
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1answer
172 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 ...
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2answers
87 views

Help with STRING database data

I'm working with data downloaded from STRING database (string-db.org) for protein-protein interactions. My idea is to compare the topology of connections of the same protein on different organisms. ...
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1answer
196 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 ...
3
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1answer
95 views

Simplified molecular-input line-entry system

This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer. What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is ...
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2answers
79 views

Sequence compression method / format

As someone working with sequencing data and sequence files I was wondering whether is there a compression method / format for sequence / read files? Of course one can use general compressors like rar ...
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0answers
51 views

Primer Designing [closed]

I have a basic idea about the requirements in primer designing. Basically my knowledge is limited to theoretical knowledge and have no experience in actual primer designing. And also I have a basic ...
3
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0answers
129 views

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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1answer
127 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 ...
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1answer
185 views

Blast output - program to count the number of hits [duplicate]

I have to use the old version of Blast (not Blast+) to compare DNA sequences and I have to know the number of all hits. They are not given in the header and I have to know them for many many of blast ...
2
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2answers
126 views

Local BLAST Copy Number per Hit

I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at ...
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3answers
350 views

How can I align more than 2 sequences locally?

ClustalW and Omega of EBI and Blast of NCBI, both globally align sequences. Smith waterman of EBI aligns sequences locally, but works with just two sequences. How can I align more than 2 sequences ...
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1answer
104 views

What are genome wide functional linkages?

There are two types of interaction classifications used to describe Protein-protein interactions, namely physical and functional. Whilst physical interactions are obvious in nature and methodological ...
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1answer
207 views

What sample sizes are ideal for carrying out Bayesian Skyline Plots?

I am interested in creating Bayesian Skyline Plots to look at demographic changes in certain population groups. However, these populations have very little within population variation. Around 5 ...
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1answer
28 views

RNA-Polymerase III transcribed genes

I have a list of differentially regulated genes from a high-throughput experiment of the human genome. I would like to find out which of these genes are transcribed by a RNA polymerase III and which ...
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2answers
187 views

The meaning of RNA-seq data

many papers I read mentioned "RNA-seq data". While searching for the meaning of this word, I could not find any layman's definition. As far as I understand, RNA-seq data is the complete RNA ...
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1answer
68 views

Protein PTM site prediction

Is there any in silico analysis method to predict post-translational modification sites on a given protein?
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2answers
108 views

Can all biological processes be understood as computations and studied as such? [closed]

Can we understand a cell as an organic computational device? In that case the whole organism can be considered an ensemble of a large number of interacting computational devices? If this is the ...
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1answer
33 views

What are host cellular factors?

With respect to this paper: Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication What does the term "host cellular factors" mean??
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1answer
38 views

How to predict the top microRNAs that bind to 3`UTR of a specific gene [duplicate]

I would like to know whether someone could tell me 1) some of the online programs that will predict the top microRNAs that bind to 3`UTR of a specific gene (for eg-GAPDH). I am relatively new to ...
8
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2answers
1k views

How to find miRNA binding sites on a specific gene?

I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? ...
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2answers
1k 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 ...
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5answers
11k views

Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO?

Does DNA have anything like IF-statements, GOTO-jumps, or WHILE loops? In software development, these constructs have the following functions: IF-statements: An IF statement executes the code in a ...
3
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1answer
228 views

meaning of the “reads” keyword in terms of RNA-seq or next generation sequencing

I'm an undergraduate student at computer science and currently, I'm interested in bioinformatics. Today, I've started to read a paper about clustering and classification of non-coding RNAs can be ...
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0answers
61 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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1answer
70 views

interpreting enhancer and promoter regions of a target gene

I am reading a paper which talks about promoter/enhancer regions of certain protein coding genes. These genes are for which evidence points to having strong MEF2 transcription factor binding sites. ...
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0answers
52 views

How do I use BEAST for divergence time estimation in this case?

I am interested in using BEAST to find the divergence time estimates of species separations within a genus of frogs. The genus separated from a outgroup taxon I have chosen around 80 million years ...
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1answer
63 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 ...
2
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1answer
286 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
95 views

Protein Structure Parameters

I'm wondering about the minimal set of parameters necessary to define a protein's structure. My understanding is that the backbone geometry is defined by the phi and psi angles (torsion angles), and ...
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0answers
28 views

EMBOSS matcher and supermatcher - incongruent results?

I am trying to align a sequence to the mouse genome. I know a priori that part of my sequence should align to chromosome 9, but not all of it. I gathered that EMBOSS' ...
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0answers
52 views

how to extract promoter regions given a TF binding site

I have constructed a PWM and want to test its accuracy. Scanning an entire chromosome (chr3, hg18) yields very high false positives (magnitudes higher than the true positives). Scanning the entire ...
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0answers
25 views

How can I classify Breast Cancer if I have incomplete receptor information?

I have a clinical data table for a cohort of Breast Cancer patients and I want to classify them as being either triple negative or triple positive. You can find the file here. For some of the ...
4
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1answer
104 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 ...
2
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1answer
102 views

Stockholm format to dot-brackets format?

I need to convert all my sequences in a Stockholm format into this: ...
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2answers
63 views

All UniprotIDs of a cancer pathway

I need to download all uniprotIDs of a cancer pathway, say the AKT Signaling. It may be super easy, but I don't know which resource to look at since it is a new field. How/where do I find these?
9
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1answer
769 views

How are we able to find the specific sites at which DNA binding proteins bind?

We know that some DNA binding proteins are site specific, that is they recognise and bind to a specific nucleotide sequence. My question is how can we precisely tell at which sites they bind? Is it ...