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
23 views

“miRNA binding sites in the 3'UTR region and transcription factors binding site in the promoters of a specific gene”? [on hold]

What does it mean when we are been asked about "miRNA binding sites in the 3'UTR region and transcription factors binding site in the promoters of a specific gene"? We will use databases like ...
0
votes
0answers
25 views

How do I import FASTA files into Haploview?

I'm trying to produce a haplotype network and so have decided to use the software haploview. However I'm having some problems importing my sequences into the software. I Have my sequences in a FASTA ...
8
votes
1answer
50 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 ...
2
votes
1answer
22 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?
0
votes
1answer
31 views

STRING ID - allelic differences and splice variants

STRING has protein (amino acid sequences) mapped to a single gene ID. I have these doubts with respect to STRING ID. I find that 1.All alleles of a single gene share the same STRING ID and ...
-4
votes
0answers
42 views

What are the 5 most expensive machines that can be found in a bio-lab? [closed]

What are the 5 most expensive machines that are specific to a biology laboratory? In this case the type of biology laboratory that specialises in molecular biology and bioinformatics (study of cell ...
8
votes
1answer
63 views

How to validate the regulatory interactions inferred from gene expression data?

My algorithm learns regulatory interaction between genes using Bayesian Network approach from gene expression data. After the algorithm has converged to a network of interacting genes, how to validate ...
2
votes
3answers
93 views

fastq-dump using mkfifo to stream data

So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk. I'm curious whether ...
0
votes
0answers
19 views

How to check HCV genomic sequences between Two samples is different or not? [on hold]

I am looking to determine if the Hepatitis C Virus genomic sequences (variant population structure) between two samples is different to a statistically significant degree. If the nucleotide ...
0
votes
0answers
37 views

From a list of protein accessions, how can I retrieve DNA sequences from GenBank?

I have 1000's of protein sequences in FASTA/their accession numbers. I want to go back into the whole genome shotgun database and retrieve all DNA sequences that encode for a protein greater than or ...
0
votes
0answers
18 views

How to do an alanine scan using Rosetta?

I have a complex of two proteins interacting. I define their interface of interaction as the set of residues that are less than 5 Angstroms from each other. I want to do an alanine scan on one of the ...
1
vote
0answers
29 views

plot the nucleosome distance to TSS [closed]

I am new to bioinformatics and python,Now I have downloaded nucleosome-seq data and TSS-seq(which also names CAGE) data,so I try to draw a picture like this: ...
1
vote
1answer
37 views

Is there any way to make pymol find the closest distance between RESIDUES? [closed]

This seems like an obvious utility, but I can only make it find the closest distance between ATOMS, which makes a big mess on the screen. Edit: To be clear, I want to find the closest distance ...
0
votes
2answers
46 views

Counting the number of hydrogen bonds of multiple PDB files

I've been trying to figure out a systematic way to count the number of hydrogen bonds for multiple PDB files. DSSP shows me the total number of hydrogen bonds when I make ...
4
votes
1answer
49 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 ...
2
votes
1answer
60 views

what the best E-value cutoff in the miRNA homology search

I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop ...
6
votes
1answer
148 views

Find protein homologs with BLASTp

I'm trying to find homologs of a set of proteins using BLASTp. I'm working with custom databases. I'm using evalue of 0.00001 as threshold. I would like to filter queries having hits with >90% ...
2
votes
1answer
24 views

Gene Sequencing and Plasmapper

Is there anything similar to this in Java (especially the circular map sequencing along with hover effect)? For information I would like to convey that I am using Plasmapper and BioJava for achieving ...
1
vote
1answer
36 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 ...
3
votes
1answer
57 views

What information can Uniprot give me about phosphorylated forms of proteins?

I have a list of proteins formatted like this: ...
-2
votes
1answer
43 views

Why the name coined for MARKUP LANGUAGE for SBML? [closed]

I'm get the confusion about SYSTEM BIOLOGY filed. SBML is refer to as SYSTEM BIOLOGY MARKUP LANGUAGE why we should called as ...
3
votes
1answer
62 views

Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?

Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge ...
3
votes
1answer
119 views

Hamming distance between two DNA strings

By definition from Wikipedia, the Hamming distance between two strings of equal length is the number of positions at which the corresponding symbols are different. In other words, it is the number of ...
2
votes
1answer
37 views

Sequencing a specific region of a genome

First off, I'm new to bioinformatics and I am learning about DNA sequencing. Let's say that I knew that a specific region of a genome which contained information about a disease (whether it a person ...
8
votes
2answers
105 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)? ...
1
vote
2answers
62 views

What kind of technology is required for plant seed DNA printing? [closed]

I'm a programmer so I have little knowledge in the field of biology. However I have an interest in plants, GMOs and DNA (in terms of programming). So, I want to know what kind of technology is ...
1
vote
1answer
42 views

How can I compare the STRIDE and DSSP output files of a particular pdb file?

I have the pdb file of H-ras protein 5P21.pdb. I am supposed to compare the output of DSSP and STRIDE files after feeding this pdb file to respective servers. My question is how to make a quick ...
0
votes
1answer
29 views

Cardiac Excitation Threshold - in C++ modelling [closed]

So I am trying to write a code in C++ about the cardiac excitation threshold. I know that this excitation threshold is the shortest stimulus2 value at which it can conduct an action potential (known ...
6
votes
0answers
168 views

Additive genetic variance components from LMER in R

I've set up some dummy data in R which makes 40 genetically related lines, they are all siblings within a line so are genetically related by a factor of ½ thus additive genetic variance should be ...
3
votes
1answer
51 views

PSI-BLAST website algorithm parameters

http://blast.ncbi.nlm.nih.gov/Blast.cgi In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? ...
1
vote
0answers
60 views

Suggestions of famous experiments with plant cells? [closed]

I am looking for examples of famous experiments with plant cells. Ideally, the experiment would use: bright-field microscopy staining include several compared groups, so that e.g. one-factor ...
2
votes
0answers
37 views

Biology Experiment Data (Hodgkin-Huxley)

I'm doing research into the Hodgkin-Huxley Model from an electronics/mathematics perspective and I'm looking to find actual numerical results from experiments on squid axons. I want to compare the ...
2
votes
1answer
81 views

Bowtie: cannot read fasta file?

I am trying to use bowtie2 to analyze my data in FASTA format, but it seems that this version can't read properly my data. My command line is as follows: ...
1
vote
1answer
57 views

Modeling intracellular interactions between sender and receiver bacteria

I am involved in a modelling task of a biological process described as follows: -- "Objective: to model behavior of a sender receiver type system The process goes as follows Pre-signal [PS] is in ...
0
votes
1answer
70 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
1answer
49 views

BLASTn vs ORF tools

Sequencing projects sequence one strand and call that the + strand and then extrapolate the sequence of the - strand. This means that sometimes the genomic sequence that you download from a database ...
2
votes
2answers
66 views

peptide MHC microarray

"The recent technology is peptide–MHC microarray or artificial antigen-presenting chip. In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a ...
1
vote
1answer
24 views

PDB file SEQRES have different datas?

In PDB file, SEQRES represent the aminoacids but some pdb file present the "GLC" and some other. for example ...
5
votes
2answers
172 views

How can I text-mine full-text articles from PubMed?

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 ...
0
votes
0answers
19 views

transfection of expression library made from cDNA into cells expressing the desired MHC haplotypes [on hold]

http://www.sciencedirect.com/science/article/pii/S0167569997800205 If anybody has access to this paper, can you please explain me the process to find TAA based on transfection of expression library ...
2
votes
1answer
41 views

Data Bias in protein-protein interactions data

Databases like STRING have so many predicted as well as experimental interactions data for many organisms.However there is a bias in the data which they have?. a)The first is gene co-occurrence ...
-2
votes
1answer
46 views

What is hTAP?? Please help

Could not find a single article regarding this. What is hTAP? Tap is Transfer associated protein, that I know, but what is hTAP??(I have not studied biology since last 8 years and now I am going ...
0
votes
1answer
45 views

How can I download a gene sequence from GenBank (NCBI)? [closed]

Could you tell me the steps to find and download a gene sequence from GeneBank? I would appreciate your help.
2
votes
1answer
57 views

Difference between sequential and conformational epitope

Is the difference only in its structure? Like conformational epitope has 3D structure while sequential has a linear structure?(I have not studied biology since last 8 years and now I am going through ...
0
votes
0answers
24 views

MHC restricted peptide

What is an MHC restricted peptide? "MHC-restricted antigen recognition, or MHC restriction, refers to the fact that a given T cell will recognize a peptide antigen only when it is bound to a host ...
4
votes
2answers
85 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 ...
7
votes
2answers
122 views

RNA-Seq library construction challenges: the biases of RNA fragmentation vs cDNA fragmentation

I recently watched a presentation on RNA-seq that covered some of the choices one can make along the way, and I didn't fully understand one of the choices in particular. Near the beginning of the ...
2
votes
2answers
45 views

Simulating Drug Entry in Protein and binding?

Is there any simulation protocol or paper which can simulate the dynamics of drug entry and interaction with the target protein?
1
vote
0answers
27 views

Segregation Analysis for predicting age-specific cancer risk [closed]

I am relatively new to the world of genetics research and have been tasked with presenting to my lab the potential value of a paper that uses Complex Segregation Analysis for a risk analysis. The hope ...
0
votes
1answer
52 views

Nucleotide sequence for STRING protein sequence

I have protein sequences from STRING database: The amino acid sequence files are like this: 4932.Q0010 (Saccharomyces cerevisiae) ...