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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What are the characteristics of a promising drug target?

When researchers are looking to start developing a drug, what characteristics do they look for in the potential proteins (assuming they already have good quality structural models)?
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661 views

Batch convert miRNA names to Accession IDs?

Does anyone know of tools to convert lists of miR names to their miRBase Accession IDs? I know they exist, but my search keeps pulling up gene ID converters. EDIT: both @rg255 and @shigeta have ...
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27 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 ...
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1answer
31 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 ...
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32 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, ...
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66 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 ...
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50 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 ...
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93 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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52 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 ...
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1answer
27 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 ...
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1answer
20 views

Microarray probe and target

In a microarray, which one is called a target and which one is the probe? the one that is added later , is that the probe or the one present in the slots of the microarray, that is the probe? (I have ...
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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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92 views

Convert gene name to uniprot ID

i have a list of gene name in a file CHRNB2 EGR2 GCK KRT14 LMNA FGF3 TK2 ABCC8 How can I map them to uniprot ID ? P.S I tried Uniprot "ID mapping" ...
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111 views

Heterochromatin binding sites position information

I am working on a project and I'm trying to find data on the position of genes and heterochromatin binding sites such as HP1 in Drosophila melanogaster. Is this information available for the DGRP ...
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1answer
38 views

Alleles notation in SNPPedia criteria

I can understand the allele notation when is in the form rs8176719(T;T) or rs8176719(G) but recently i found this ones rs8176719(T;-) or rs8176719(-;T). So im confused, rs8176719(T;-) is the same as ...
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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 ...
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1answer
64 views

downloading a reference genome for alignment

I am currently working through the code example on the MATLAB website. It requires me to download the reference genome of Arabidopsis thaliana (thale cress) so I can use BowTie2 to align the Chip-Seq ...
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1answer
45 views

About the quality of microsatellites

I built a script to detect microsatellites in a FASTA file. However, there are thousands of possibilities. So, my question is: what are the markers of a "good" or "useful" microsatellite? - How ...
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47 views

What is the close and related genome used for in Gene models?

all I am a little bit confused about using the related genome or reference genome. When we have a reference genome, we can do alignment. Also we can do the assembly. Can you give some more reason ...
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34 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 ...
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56 views

Why are low throughput methods more trustable for protein interaction?

I read that protein interactions found using high throughput methods are less trustable than those found using low throughput methods. For example, searching for interaction of BRCA2 on BioGRID, I ...
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1answer
62 views

Hidden Markov Model

I read about the hidden markov model in bioinformatics. I amn't able to understand what it is. Can anyone explain me in brief and in very very simple words what it is ? I have NO background in ...
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2answers
259 views

Blast a sequence against multiple databases

I would like to BLASTP a list of protein sequences in fasta format against multiple protein databases. Since I'm only interested in the first hit of each database, it is possible that BLAST result ...
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1answer
77 views

(Web)app to search metabolic/signalling pathways

I'm looking for an application where you can find pathways by selecting a chemical occurring in it. So, for example, selecting 6-phosphogluconolactone brings up the pentose phosphate pathway or any ...
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1answer
48 views

Where can I find pdb files for macromolecules like receptors?

I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.
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59 views

Isoprenoid Diphosphate Concentration in Yeast saccharomyces cerevisiae

Isoprenoid Diphosphate(IPP) is an important metabolites which is precursor in lot of secondary metabolites like Dolichol diphosphate, ubiquinone, prenylated proteins and carotenoid (not synthesized ...
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1answer
91 views

Modeling yeast biochemical pathway using enzyme kinetics

I need enzyme concentration and metabolites concentration values to en-corporate these values in my model and do some simulation. I searched through some database yeast metabolome database ...
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1answer
66 views

Information Gene HBA2

Gene : HBA2? hemoglobin alpha 2 (Homo sapiens) I don't find any tissues (or organs) in which the expression of this gene is strongest? What is the size of the gene (promoter off) encoding this ...
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1answer
236 views

Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. The ssm is in the following format: ...
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1answer
93 views

Confusion related to the use of PCA to determine the background network

I was reading this paper related to use of gene expressions for predicting the drug response. I have this confusion, the paper has used PCA on the covariance matrix formed by the genes to get what is ...
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1answer
79 views

Recombination-based vs. Sequence-based genetic mapping

Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping? I think that in the past recombination-based ...
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1answer
35 views

Where can I find a transcriptome of a normal uveal melanocyte?

I am looking for a database where I could find a transcriptome (say obtained with a microarray analysis) of one (or ideally many) normal uveal melanocytes ?
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1answer
75 views

TFBS predictions for yeast and pombe?

Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like ...
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30 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. ...
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22 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
58 views

Modelling how much cadmium a cell will be able to chelate with phytochelatins

I am involved in a synthetic biology project where I have to do modelling with ODEs. The biological process I want to model is the chelation of Cd2+ with phytochelatins, to know how much can be ...
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80 views

Workflow for batch analysis of ROI in histology samples

This is a pretty big task, and I have several work-arounds, but I am looking for an efficient way to go from PAS stained slides of lung tissue to defined ROI's over the whole slide (presumably via ...
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0answers
35 views

Visualizing secondary RNA structure binding to target

I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but ...
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58 views

Reverse complement of reconstruction model for assembling reads

One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
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5answers
100 views

How much does a typical biologist know about signal processing, machine learning, and (theoretical) computer science? [closed]

How much does a typical biologist know about signal processing, machine learning, and (theoretical) computer science? Coming from a neuroscience background where knowing about algorithms and computer ...
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1answer
47 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.
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1answer
107 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 ...
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3answers
89 views

Phylogenetic tree

I want to find the conventional phylogenetic tree of human, mouse, C elegans and drosophila, without all the other organisms. Do you know where can I get it? thanks, Noga
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73 views

What is the datatype of dna sample?

What is the type of data you get when analyzing dna of a person? If you want to store them in a database, what type of field you will need (text,number,hex)? And what should be it's length?
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137 views

Problem on finding sequence of Taq polymerase

As i know, Taq Polymerase can be found in Thermus aquaticus, so i do a search for protein list of Thermus aquaticus and have this : http://www.ncbi.nlm.nih.gov/genome/proteins/1724?project_id=55053 . ...
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1answer
51 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. ...
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1answer
54 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) ...
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1answer
60 views

Can someone suggest me good opencourseware links for learning computational biology basics?

My internet is slow and I have only 1GB data usage allowed for this month. And I want to make maximum out of it for learning some basics of computational biology. Which are the best online course ...
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2answers
62 views

is there a way to do batch download for all gene pathways?

I would like to download all the gene pathways and genes of each pathway. Preferably, gene length of each gene as well. It would be a lot more convenient if there is an R package.
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How to get conservation of vaccine candidates between hundreds of bacterial strains?

We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about 200). I would ...