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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25 views

Difficulties understanding a pathway

I am not a biologist and I would love to understand what is going on with this pathway conclusion. I went to the description but still it is complicated and I could not follow. Can someone please help ...
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2answers
29 views

Which information can be obtained from a list of gene names?

Lets say I only have a list of gene names. I know they are up regulated and I know they are related to cancer. What information can I obtain from having only the names of genes? For example is there ...
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0answers
26 views

How to run Mugsy software on Linux Ubuntu 11.04? [on hold]

How to run Mugsy software on Linux Ubuntu 11.04? I can`t run it as written in instructions How to set up .sh file with installation path correctly? Here is my effort to set it up: #!/bin/sh export ...
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1answer
46 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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0answers
43 views

Use genetical modification to produce quantum computer? [closed]

Is it theoretically possible to use organism modifications in order to make it produce molecules capable of forming Qbits, therefore performing quantum computing. Instead of constructing Qbits ...
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2answers
47 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
35 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 ...
2
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0answers
33 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: ...
2
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0answers
23 views

Finding confidence level of miRNA disease associations

I'm an undergraduate computer engineering student, and I have a project about bioinformatics. In this manner, I need to find prediction( or association I'm not sure the correct terminology) confidence ...
1
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1answer
35 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 ...
8
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4answers
170 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 ...
3
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0answers
57 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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1answer
93 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 ...
8
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1answer
71 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 ...
5
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2answers
47 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. ...
1
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1answer
18 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 ...
3
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1answer
65 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 ...
2
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1answer
24 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
70 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 ...
5
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2answers
78 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 ...
2
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1answer
22 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
25 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 ...
4
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2answers
153 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 ...
3
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1answer
53 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 ...
53
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5answers
10k 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 ...
2
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0answers
45 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 ...
0
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1answer
33 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
21 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 ...
1
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1answer
42 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 ...
1
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1answer
45 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. ...
3
votes
2answers
39 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 ...
0
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1answer
76 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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0answers
15 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
27 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
16 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 ...
2
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2answers
53 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 ...
2
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2answers
57 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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0answers
28 views

Where can I find mutation datasets for cancer (other than TCGA)?

My lab has been using TCGA data (somatic mutations and clinical data) to develop panels of genes and of mutations we expect to see in certain cancer populations. We'd like to validate our panels by ...
4
votes
1answer
63 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
votes
1answer
43 views

Stockholm format to dot-brackets format?

I need to convert all my sequences in a Stockholm format into this: ...
1
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0answers
21 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 ...
1
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2answers
70 views

What is the meaning of dots and dashes in clustalw?

I am converting outputs in stockholm format to clustalw using ...
5
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1answer
52 views

Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss. I am only looking at a small ...
0
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0answers
23 views

Explanation of sequence motif diagram given in wikipedia [duplicate]

can someone please explain me this graph?? I did not get what information content is in this graph means. Does the size of the letter indicate that higher chance of that letter to be present in that ...
8
votes
2answers
57 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?
3
votes
1answer
104 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 ...
9
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1answer
386 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 ...
6
votes
1answer
42 views

What is a positive epitope fragment

What is a positive epitope fragment? I found one paper on the subject: COBEpro: a novel system for predicting continuous B-cell epitopes by Michael J. Sweredoski and Pierre Baldi
2
votes
2answers
59 views

How to retrieve full gene names list and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any)?

How to retrieve full gene names and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any other software or language)? Is it possible vice versa: having full gene ...
1
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1answer
53 views

How do you convert mtDNA sequences in FASTA to FSTAT format?

I've got control region sequence data from a population of shark and I'm looking to convert this from FASTA to FSTAT in order to calculated the effective population size of females. The software I ...