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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6
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1answer
95 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
210 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 ...
-2
votes
1answer
46 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
97 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
180 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
140 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
39 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
vote
2answers
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 ...
10
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3answers
240 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
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 ...
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
votes
1answer
34 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
votes
1answer
142 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 ...
2
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0answers
39 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
92 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: ...
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 ...
7
votes
2answers
134 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 ...
13
votes
4answers
292 views

Machine learning for light microscopy — problems to solve?

I would like solve some biological problems that would improve the state-of-the-art of biology or bioinformatics. In particular, I want to apply machine learning on light microscopic images. The ...
1
vote
1answer
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 ...
1
vote
1answer
96 views

Datasets of aligned nucleotide sequences [closed]

Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there? (I would like to use such datasets for training the alignment ...
-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 ...
5
votes
2answers
200 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 ...
1
vote
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 ...
0
votes
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.
2
votes
1answer
84 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
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0answers
25 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 ...
2
votes
2answers
47 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?
0
votes
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) ...
4
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2answers
46 views

where to find the relative frequency distribution of synonymous codons

Most amino acids can be encoded by more than one codon. For example, Serine can be encoded by any one of ...
3
votes
1answer
41 views

SEREX serological analysis of cDNA expression library

What is Serological Analysis of cDNA expression library? I went through this article:http://cancerimmunity.org/serex/introduction/ but could not really make out. Can someone please explain this to me ...
1
vote
1answer
252 views

What is the difference between second and third generation sequencing

I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to ...
0
votes
1answer
23 views

Degenerate Alignment Analysis

Can someone please tell me what is Degenerate alignment analysis? Could not find a good article on the internet that could help me understand what it means? (I have not studied biology since last 8 ...
1
vote
2answers
126 views

What is most simple eukaryotic genome?

Expressed in number of Base Pairs or Bytes, about how large is the simplest eukaryotic genome? How much of this is 'junk-DNA' (non-coding)?
1
vote
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 ...
0
votes
0answers
27 views

TAA- Tumor associated antigen [duplicate]

An approach to find Tumor associated antigens is based on transfection of expression library made from cDNA into cells expressing desired MHC haplotypes. Can someone please explain what this line ...
1
vote
2answers
58 views

Where to find the corrected BLOSUM matrices?

I was looking at this paper which talks about the miscalculations in the BLOSUM matrices and how the "wrong" BLOSUM62 matrix performs better than the corrected version. I was trying to find the ...
1
vote
3answers
92 views

Are there tools for automatically parsing glycan names into tree structures?

My colleague and I are working on a project involving data produced at a glycan microarray facility. The array data that came back to us were a list of glycan names (in IUPAC condensed format). We ...
2
votes
1answer
68 views

Heterozygosity and the Wright-Fisher model

I was reading the textbook Probability Models for DNA Sequence Evolution by Durrett. In chapter 1, he discusses the Wright Fisher model and the coalescent theory ...
1
vote
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 ...
2
votes
0answers
29 views

Genome-wide methylation analysis: sources of technical error?

We are doing a genome-wide analysis of methylation via bisulfite sequencing for an insect species. Previous experimental techniques have suggested the presence of methylation in this organism, ...
0
votes
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 ...
4
votes
3answers
152 views

Does anyone know a good software for producing tanglegrams?

I'm trying to look at relationships between parasite and host phylogenetic trees. I have done a bit of searching for a software in which to do this with, and I have tried using Dendroscope and ...
2
votes
0answers
36 views

What does the term 'epitope mapping' mean? [closed]

Epitope mapping means identifying the binding site of antibodies on the target antigen. This means that the site to be identified is part of the antigen and not antibody, am I right?
2
votes
2answers
90 views

How do I perform recurring pattern mining or regular expressions of nucleotide sequences?

I am interested in performing nucleotide sequence pattern-mining (regular expressions) which is 12 characters (sequences) in length from a dataset. Is that possible to script using MATLAB?
8
votes
2answers
822 views

Scoring sequence against position weight matrix

I have a weight matrix of length 20 x 15 (amino acids x sequence positions). Each element of my weight matrix is a relative probability If I have a sequence say "AAPGTGASMHSGLLW" how would I score it ...
2
votes
1answer
145 views

Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions

I am working with RNA-seq data from the Cancer Genome Atlas TCGA and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk ...
2
votes
1answer
54 views

How can I view modENCODE data faster?

I am trying to view several data tracks in the modENCODE GBrowse genomic browser. However, the site is so slow, it is practically unworkable. Is there a faster way to explore the data?
1
vote
1answer
57 views

Genome Assembly Using Reads

I'm taking an online bioinformatics class and I am stuck on a problem. The resources I have found don't help that much. Here is the problem: "Assemble the error-free reads from a circular genome on ...
1
vote
2answers
203 views

Draw simplified phylogenetic tree for kids

I need to draw simple, phylogenetic tree for kids lecture. I am looking for an online tool where I can enter organisms (e.g., human, wasp, fungus) and get figure of a phylogenetic tree. Tree should ...
1
vote
1answer
50 views

How to selectively download 3 fields from every record in UniProtKB?

I want to download a comprehensive table of protein names from uniprot.org. More precisely, I want to generate a tab-delimited table consisting of the id ...