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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74 views

Downloading specific yeast genes in an automated manner?

I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, ...
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0answers
15 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 ...
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1answer
85 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 ...
3
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1answer
56 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 ...
8
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1answer
63 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 ...
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0answers
33 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 ...
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2answers
94 views

positive and negative feedback

I want to know more about positive feedback in gene regulation and to know the similarity and differences between positive and negative feedbacks.
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3answers
95 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 ...
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0answers
31 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 ...
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1answer
33 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 ...
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0answers
171 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 ...
4
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1answer
218 views

Software for counting fly eggs

Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid ...
8
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1answer
66 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 ...
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1answer
27 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?
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4answers
227 views

Is there a PSI-BLAST for nucleotide sequences?

I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs ...
1
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1answer
38 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
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0answers
42 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 ...
1
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1answer
33 views

Degenerate primer design for DIG in situ hybridization

New to molecular and have learned to design primers from google/youtube so any info would help Would someone be willing to share their protocol for degenerate primer design? Breakdown: Trying to ...
3
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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? ...
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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
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1answer
72 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, ...
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1answer
48 views

Applying Constraint Programming to sequence alignment/analysis

My Masters program is focused on formal methods such as SAT solving and constraint programming. I am interested in applying such techniques to problems in sequence alignment and sequence analysis, ...
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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
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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: ...
4
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2answers
86 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 ...
0
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2answers
47 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 ...
9
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0answers
106 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 ...
4
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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
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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 ...
1
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1answer
28 views

Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?

Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an ...
6
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1answer
149 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
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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
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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 ...
5
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1answer
90 views

Book suggestion on computational molecular evolution

I'm currently reading Computational Molecular Evolution by Yang. Can you recommend alternative books? I am finding it to be lacking on conceptual discussion (it's more focussed on the mathematics and ...
6
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2answers
201 views

Can forensic DNA analysis be used to generate a visual approximation of a suspect?

In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
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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
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1answer
63 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
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1answer
122 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 ...
8
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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)? ...
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 ...
1
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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 ...
10
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3answers
235 views

Shortest strings not present in the human genome

What length are the shortest strings of DNA not present in any known person's genome, and what are they? And is there a database online by which I could find this out?
1
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1answer
44 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 ...
2
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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 ...
0
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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 ...
9
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1answer
139 views

Comment on the introduction to a bioinformatics paper

I've written a paper about DNA sequence analysis. This paper attempts to use Bayesian modelling for a set of DNA sequences. It will probably end up either in a statistics journal, or, more likely, in ...
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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
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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 ...