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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4
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1answer
82 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 ...
1
vote
1answer
84 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 ...
3
votes
0answers
66 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 ...
2
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2answers
92 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 ...
9
votes
3answers
236 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 ...
0
votes
1answer
96 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
votes
1answer
142 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 ...
1
vote
1answer
22 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 ...
5
votes
2answers
116 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
votes
1answer
43 views

Protein PTM site prediction

Is there any in silico analysis method to predict post-translational modification sites on a given protein?
0
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2answers
86 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 ...
2
votes
1answer
32 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??
0
votes
1answer
30 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
votes
2answers
460 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)? ...
4
votes
2answers
232 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 ...
62
votes
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 ...
3
votes
1answer
85 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 ...
2
votes
0answers
55 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 ...
1
vote
1answer
46 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. ...
1
vote
0answers
28 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
vote
1answer
46 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
votes
1answer
98 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. ...
2
votes
2answers
68 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 ...
1
vote
0answers
20 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' ...
1
vote
0answers
40 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 ...
0
votes
0answers
21 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
votes
1answer
70 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
69 views

Stockholm format to dot-brackets format?

I need to convert all my sequences in a Stockholm format into this: ...
1
vote
0answers
26 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 ...
2
votes
2answers
157 views
8
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2answers
60 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
votes
1answer
504 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 ...
0
votes
0answers
24 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 ...
2
votes
2answers
91 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 ...
6
votes
1answer
49 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
4
votes
1answer
70 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
2answers
178 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 ...
0
votes
2answers
232 views

How to do whole genome sequence alignment in R or Ruby/C++, any good language? [closed]

I need to perform tuberculosis mutation analysis. First step I need to do is to align sequences in fasta format against one reference file. i tried CLC genomics workstation --- it hangs on 60 000 ...
0
votes
0answers
81 views

How to build gene interaction network based on correlation between gene expression values using software like Cytoscape and R?

How to build gene interaction network based on correlation between gene expression values using software like Cytoscape and R or smth else? I have .tab with gene names and total expression values. ...
0
votes
0answers
34 views

What log transformation and normalization functions are most commonly used for microarray and how to select them?

Need help on rational approach to choosing log transformation, standartization and normalization functions in microarray experiments. I am using Expander software and it provides Log2 transform and ...
0
votes
1answer
96 views

What to do if microarray t-test, ANOVA, SAM and LImma show various selected significant genes?

Need advice: how to approach discrepancy in differential microarray gene expression test results: what to do if ANOVA, ttest, SAM and Limma procedures show different results and especially more ...
0
votes
1answer
60 views

How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis

I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be ...
2
votes
1answer
84 views

Whole genome sequence analysis software

Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, ...
1
vote
2answers
77 views

Aligning multiple sequences in heterogeneous group

I have a list of ~200 DNA sequences, representing probably 50 different genomic regions but they're all mixed up. For example, if I have seq1, seq2.... seq10, ...
13
votes
2answers
735 views

Human disease and associated phenotype database?

Does anyone know of any good databases that contain symptoms for diseases and other ailments in humans? I've tried working with UMLS, but thats been impossible to work with. I've also tried working ...
10
votes
1answer
136 views

Using the IMGT/GENE-DB service to find RSS

I'm trying to get the data for the Human and Mouse 12 and 23 Recomination Signal Sequences (RSS), to run a classification algorithm on it. I'm not a biologist, so I apologise in advance for my ...
0
votes
1answer
56 views

Supercomputer and undergraduates [closed]

Is it common for an undergraduate to run their thesis (evolutionary genomics) in a supercomputer? In my country, few supercomputers exist, but I'm not sure how it is for bachelors in the US or Europe. ...
1
vote
1answer
473 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 ...
1
vote
1answer
141 views

Distance matrix with different length sequences

In a project we're doing (in python), we want to create a distance matrix for a phylogenetic tree with multiple, different length sequences. However, what we've seen so far (AlignIO in biopython, ...
1
vote
0answers
25 views

What genetic distance model should be used when calculating genetic differences in Arelquin?

I'm using Arelquin to look at the genetic structure between a number of different populations. I want to compare the populations by producing pairwise FST values, however I don't know what model for ...