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 ...

learn more… | top users | synonyms (1)

0
votes
0answers
26 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?

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
votes
1answer
60 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 ...
0
votes
1answer
22 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. ...
0
votes
0answers
14 views

What are the forms of host pathogen interaction [on hold]

What are the forms of host pathogen interaction apart from the host pathogen protein protein interaction?? Or is protein protein interface is the only one way of host pathogen interaction?? I am ...
1
vote
0answers
16 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
37 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
vote
1answer
41 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
22 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 ...
31
votes
4answers
2k views

What exactly are computers used for in DNA sequencing?

I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing. There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts. ...
0
votes
0answers
26 views

Aspects of host pathogen interaction [on hold]

I have very simple(probably silly) question. I am a bit confused, hence asking. Does the epitope mapping fall under host pathogen interaction? What I want to know is what are the aspects of host ...
2
votes
2answers
50 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 ...
0
votes
0answers
12 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' ...
0
votes
1answer
22 views

What does gene encoding receptor mean? [closed]

What does gene encoding receptor mean? I know what each of these of these words separately, but cant identify the exact meaning of the complete phrase, I cant visualize. Please help me!
0
votes
0answers
23 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 ...
3
votes
1answer
31 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
votes
0answers
14 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 ...
1
vote
2answers
50 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 ...
4
votes
1answer
61 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 ...
0
votes
0answers
18 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 ...
2
votes
1answer
38 views

Stockholm format to dot-brackets format?

I need to convert all my sequences in a Stockholm format into this: ...
1
vote
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
vote
2answers
56 views
3
votes
1answer
101 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 ...
8
votes
2answers
55 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
351 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
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 ...
1
vote
1answer
44 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 ...
2
votes
2answers
52 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 ...
-2
votes
0answers
30 views

Protein x-ray crystallization reference for bioinformatics [on hold]

I am looking for references or tutorials which introduce the field of protein x-ray crystallization, but without going into all the experimental details. I just want to learn whatever is relevant for ...
6
votes
1answer
36 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
66 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 ...
5
votes
2answers
140 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 ...
1
vote
2answers
162 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 ...
1
vote
0answers
45 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
25 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
36 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 ...
1
vote
1answer
35 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 ...
3
votes
1answer
48 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
65 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, ...
12
votes
2answers
700 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 ...
9
votes
1answer
125 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
53 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
386 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
111 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, ...
0
votes
1answer
39 views

how to reconcile PDB structures' sequences via Uniprot references?

i’m trying to reconcile structures in PDB entries with their sequences as reported in their chemList.polymer.dbref entries. E.g.: considering structures for HIV ...
0
votes
0answers
14 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 ...
2
votes
2answers
82 views

Downloading specific yeast genes in an automated manner?

I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, ...
1
vote
0answers
26 views

Download FunCat Database for Programmatic Access

I am enriching RNA-seq data for the fungus Neurospora crassa and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other ...
0
votes
1answer
114 views

Clustal Omega - convert from distance into # of substitutions

I have a set of nucleotide sequences for which I have aligned using Clustal Omega. In particular, I performed a full alignment, and obtained a full distance matrix. The distance matrix scores range ...
8
votes
1answer
86 views

Mass spectrometry versus western blotting for validation

I have mass spectrometry data (LC-MS/MS) from rat cortices under either drug or control treatments. The results were performed in triplicate (three pairs of rats, drug or control per pair). In ...