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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1answer
22 views

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

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.
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0answers
25 views

plot the nucleosome distance to TSS [on hold]

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: ...
3
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1answer
52 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 ...
4
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2answers
73 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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0answers
14 views

Is one metabolomic database more searchable than any other? [on hold]

What makes one metabolomic databases eg. HMDB more search worthy than any other? Is it possible to have a general criteria since there is not one search reason? Is there any that have more user ...
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2answers
40 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 ...
8
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0answers
86 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
43 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
44 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
124 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% ...
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0answers
38 views

tBLASTn can't find some annotated proteins. Is it possible?

Seems tBLASTn can't find some of the proteins that were annotated using PGAAP pipeline. Is it possible tBLASTn can't find some proteins? Here is the code and the results: BLASTp proteins against ...
2
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1answer
22 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
31 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 ...
2
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1answer
40 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? ...
3
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1answer
54 views
5
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1answer
87 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 ...
5
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2answers
193 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
37 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 ...
0
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1answer
41 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, ...
3
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1answer
51 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
92 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 ...
7
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2answers
82 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
61 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
231 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?
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1answer
39 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
64 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
24 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
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0answers
112 views

Calculating additive variance, heritability, and percent of variance explained by additive effects

I've set up some dummy data in R which makes 40 genetically related lines (in this case I'm simulating hemiclones - they share one haploid copy of there genome within a line, thus additive genetic ...
9
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1answer
136 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
56 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
28 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
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1answer
63 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: ...
0
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0answers
37 views

Modelling 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 ...
2
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1answer
35 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
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2answers
107 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 ...
0
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0answers
57 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, ...
13
votes
4answers
275 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
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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 ...
1
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1answer
87 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
43 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
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2answers
153 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
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1answer
22 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 ...
1
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0answers
11 views

transfection of expression library made from cDNA into cells expressing the desired MHC haplotypes

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 ...
0
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1answer
42 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
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1answer
48 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
23 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
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2answers
41 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
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1answer
50 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) ...