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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36 views

What is the difference between options protein and replication in the NCBI database?

After checking the NCBI help page, I am still unclear about the difference between protein and replication interactions for HIV. ...
3
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1answer
37 views

Which hydrophobicity scales are best for detecting transmembrane regions, and why?

There are many hydrophobicity scales for protein analysis. Broadly, I gather the differences between them are from the experimental method to acquire the data and the normalisation (or lack thereof) ...
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1answer
93 views

Design arbitrary degenerate primers (with non-binding criteria)

I would like to design a number of arbitrary degenerate primers (primers with variable bases, e.g. NGATWGCTSATNGC) for a TAIL-PCR. I would like to be able to ...
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0answers
90 views

Cut-off values for LD, LOD and D-prime as algorithmic input

I created an algorithm to generate SNPs for random people of different descents - based on HapMap data. While this works good, there is something else I want to take into consideration. So if a SNP ...
2
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0answers
71 views

Efficient algorithm to calculate various population divergence statistics

Intro and description of the data I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format ...
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2answers
82 views

Programmatic way to differentiate homodimers from heterodimers?

For pdb files is there a simple programmatic way to determine if the file is made up of homodimers or heterodimers. I have many files so an online tool or some ...
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2answers
133 views

What's read depth in VCF?

There is an attribute defined as DP (Total Depth) in VCF file format. For example, http://www.1000genomes.org/node/101. What does this attribute mean? If I get a value of like DP=128. How can be that ...
3
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2answers
101 views

Deciding a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset

Is there a methodology to select a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset, to define when there is a significative alteration? Can I download CNV data for ...
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1answer
63 views

What is enrichment? [closed]

Could someone please clarify, in layman's terms, what enrichment means? I'm currently looking at MACS and peak calling. Repeated mentions of "enriched" or "enrichment". Thanks.
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3answers
62 views

Patterns/Motifs Repository [closed]

I am new to this area. I am a researcher working on fast pattern searching in general scenarios (e.g., regex in string matching). I am curious about the "regular expression (regex)" (pattern/motif) ...
1
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1answer
501 views

best book for a comprehensive introduction to biology for a computer science graduate interested in undertaking research in bioinformatics [closed]

I have a postgraduate degree in computer science, and I wish to undertake research in bioinformatics. I had chemistry but no biology in high school. I have read bioinformatics books like "biological ...
7
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1answer
101 views

Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss. I am only looking at a small ...
3
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1answer
188 views

mFOLD prediction result interpretation

I am trying to predict the secondary structure of certain predicted pre-miRNAs through mFOLD which is the generally accepted technique for structure prediction in most studies. I am finding it hard to ...
1
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1answer
55 views

how to reconcile PDB structures' sequences via Uniprot references?

I’m trying to reconcile structures in PDB entries with their sequences as reported in their chemList.polymer.dbref entries. E.g.: considering structures for HIV ...
4
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2answers
233 views

How can I fetch nucleotide sequences based on ENA accession numbers and positions?

I have a list of ENA accession numbers and a start and end position in each sequence. In the end I want to align all those sequences, but first I have to fetch them and the list is too long to do that ...
1
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2answers
112 views

Introductory book in genetics? [duplicate]

I am working in the field of neuroscience with a background in computer science. I try to find new ways of analyzing brain imaging data (mostly MRI, EEG, MEG, fMRI) with modern machine learning ...
2
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1answer
61 views

How do I find the number of child terms associated with a specific GO term?

I am trying to figure out how to find the number of child terms associated with a specific Gene Ontology (GO) term using QuickGO, without just counting the amount of terms in a list. For example when ...
3
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4answers
350 views

Identifying the origin of replication of an unannotated *E. coli* plasmid

I have attempted a few searches for a list of origins of replication for plasmids in E. coli, but I was only able to find a list of origins, but not their individual sequences. The available plasmid ...
1
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0answers
31 views

Load specific sequences in with BioSeqIO [closed]

I am trying to load a multifasta file with Perl using my $in = Bio::SeqIO->new( -file => $entrance) and then I loop trhough the file looking for id i ...
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4answers
89 views

Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?

I did a quick search (here and elsewhere) and couldn't find anything on this subject. If all introns in a given primary transcript were spliced out in the same way, then this wouldn't matter. But ...
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0answers
43 views

Primer heterodimer problem

I design my primers in Primer3PLUS and analyze them in Oligoanalyzer3.1, A big problem that I have this is that I got very nice output in NCBI-Primer BLAST for their specificity but a very negative ΔG ...
2
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2answers
567 views

MOL2 to PDBQT conversion via OpenBabel and MGLTools removes hydrogen atoms

I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms ...
1
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1answer
37 views

Affymetrix SNP data, how to filter out rows based on rsid [closed]

This is my first time on stackexchange. I am new to bioinformatics, and I have some new SNP data from an Affymetrix Axiom array. I have the genotypes exported into a giant tab-delimited table txt ...
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2answers
61 views

What ways are there to determine how big genera are?

I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data ...
6
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1answer
60 views

Comparison of gene expression time series in vitro and in vivo

I have to analyse two datasets consisting of time-series measurements of gene expression. One set are in vivo data from the expression profiles obtained between a few days before birth to several days ...
13
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2answers
420 views

Looking for a cancer drug target database to guide sequencing of patient tumor DNA

I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s ...
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0answers
37 views

Why Pan_troglodytes-2.1.3 Assembly renamed as a Pre in ENSEMBL?

I began working with panTro3 assembly of the UCSC. This assembly corresponds to CGSC Build 2.1.3. See here: https://genome.ucsc.edu/FAQ/FAQreleases.html Now, I have to cross annotations with ENSEMBL ...
2
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6answers
152 views

Which information can be obtained from a list of gene names?

Lets say I only have a list of gene names. I know they are up regulated and I know they are related to cancer. What information can I obtain from having only the names of genes? For example is there ...
7
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2answers
457 views

What is the difference between sequence, reads, and contigs of genetic material?

Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example? I am new to bioinformatics, and I have not found any conclusive ...
8
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2answers
430 views

Is it possible to add a new sequence to a blast database without recreating it from scratch?

I have a new sequence and I want to add it to a pre-constructed BLAST database containing other sequences. The makeblastdb help does not give any hint on this regard.
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0answers
35 views

Getting read size less then specified in parameter file Flux Simulation

I have tried to use flux simulation tool to generate simulated RNA-seq data. I gave the following parameter file to flux-simulation shell script ...
0
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3answers
77 views

how to find accurately the closest species to my plant species?

I'm working on some bioinformatic analysis of a non-model woody plant within the family with least information. So, I'm looking for a closest species to my plant. Any suggestion would be highly ...
4
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1answer
78 views

Questions regarding a particular paper

With respect to the following paper: Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study I have a few questions: in page ...
4
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1answer
57 views

determining meaning of basic biological keywords about C. elegans

First of all I have to say that I have no biology background since I'm a undergraduate computer science student. Nowadays, for my research I need to use some of the databases related with ...
3
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2answers
92 views

Mass Spectrometry Terminology

I began reading this paper (http://www.biomedcentral.com/1471-2105/14/56) and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere. Consider the following ...
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1answer
67 views

What is meant by clonal isolates?

With respect to this website: http://horfdb.dfci.harvard.edu/ what does the term clonal isolates mean?
1
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1answer
202 views

An example for N50? Why do we need it?

I'm trying to understand N50 on the wikipedia. But I was unable to get a sense of the definition: Given a set of contigs, each with its own length, the N50 length is defined as the length for ...
4
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1answer
105 views

How could I identify whether given RNA-seq data is paired end or single end

I need to have a RNA-Seq dataset and therefore, I've visited the following site NCBI-geo C. Elegans In the Supplemantary file part, I clicked the SRP/SRP051/SRP051702 ftp and downloaded sra file. ...
1
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2answers
137 views

Trying to understand the big picture behind DNA sequencing, alignment and searching

I'm about to start a bioinformatics research project but I haven't any biological background. I know my project is in regards to a performance analysis of DNA sequencing and searching "weapons" like ...
40
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4answers
3k views

What exactly are computers used for in DNA sequencing?

I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing. There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts. ...
1
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0answers
54 views

Drosophila biarmipes gene annotation, transposable element?

When doing an annotation of a contig31 of Drosophila biarmipes genome, the gene predictions(in orange, red, green, tan, blue, brown, and gray) picked up numerous possible genes in the area circled in ...
2
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1answer
185 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 ...
2
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1answer
73 views

How is protein cavity centre related to binding?

I am confused and I have the following questions: 1. What are (in the context of article below) protein cavity centres? 2. How are they related to binding? (Automated identification of protein-ligand ...
0
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0answers
50 views

Determining the percentage of the query of an alignment from a BLAST output

Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that ...
4
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1answer
54 views

Multistability in the lactose ultization network

Reading the paper here, I'm confused about the production of figure 4d. The method of production is detailed in the supplementary information under the heading "Theoretical phase diagram". ...
0
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1answer
40 views

What does a read simulator do?

There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software
0
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1answer
99 views

Using Jpred to predict secondary structure

I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i ...
14
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3answers
293 views

Why reference genome is a reference?

I have heard that a reference genome such as humans is generated by randomly choosing samples from a group of donors. But why do we call the DNA sequence generated as a reference? Why should we ...
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2answers
31 views

Ribosomal DNA references sequences

I'm having a bit of trouble with searching for this piece of information. I'm doing a study related to phylogenetic susceptibility of hosts to pathogens (based on a recent Nature publication), ...
3
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0answers
47 views

How can I create R8 (homopolymer repeat) filter without using illumina pipeline?

illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and ...