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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2
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6answers
127 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 ...
6
votes
1answer
75 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 ...
6
votes
2answers
188 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
votes
2answers
344 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.
1
vote
0answers
20 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
votes
1answer
33 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 ...
10
votes
2answers
72 views

How can we predict protein folding in silico?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
0
votes
0answers
66 views

With respect to kegg website [closed]

With respect to related R class in KEGG website: http://www.genome.jp/tools-bin/relclass?RC00064 What is the biological or statistical relevance of the score? How is it computed? And does it ...
0
votes
3answers
64 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 ...
3
votes
1answer
65 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 ...
3
votes
1answer
36 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 ...
0
votes
2answers
39 views

Protein secondary structure prediction

I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling. I'm getting confused with how and when to use Jpred, swiss-mod, ...
3
votes
2answers
81 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 ...
2
votes
2answers
66 views

Do variant callers miss rare variants in reference?

Generally variant calling programs (such as GATK-UnifiedGenotyper) look for differences between reference genome and submitted sequence. However, we all know that reference genome consist rare ...
0
votes
1answer
25 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
vote
1answer
31 views

Identifying the origin of replication of an unknown *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
vote
1answer
38 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 ...
3
votes
1answer
31 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
vote
2answers
59 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 ...
37
votes
4answers
2k 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
vote
0answers
38 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 ...
1
vote
1answer
77 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
votes
1answer
61 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 ...
7
votes
0answers
69 views

Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

I experience big discrepancies when calculating melting temperature of RNA 7-mers with Biopython over values generated by a popular algorithm. I tried the nearest neighbour algorithm with RNA and ...
0
votes
0answers
25 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
votes
1answer
47 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". ...
-1
votes
1answer
30 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
votes
1answer
16 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
votes
3answers
193 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 ...
0
votes
2answers
26 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
votes
0answers
23 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 ...
7
votes
5answers
348 views

Book/source for learning bioinformatics, focused on genomics?

Does anyone know of sources for learning bioinformatics, focused on genomics? I would like to learn alot of skills I could apply potently in the workforce if I ever became adept at the fields. My ...
1
vote
0answers
52 views

Where can I find mutation datasets for cancer (other than TCGA)?

My lab has been using TCGA data (somatic mutations and clinical data) to develop panels of genes and of mutations we expect to see in certain cancer populations. We'd like to validate our panels by ...
2
votes
1answer
268 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 ...
0
votes
1answer
481 views

TCGA data, and bioinformatics design questions for SNP/ mirna analysis

It's my first time posting to this forum but was looking for some help on the data aspects of this project. My tools of choice would be in python/R . Goal: I'm looking to create a disease specific ...
1
vote
1answer
254 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: ...
0
votes
1answer
91 views

How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median

I want to transform a TCGA mRNA expression matrix (in linear data format) to log2-ratios and then run a feature (gene) selection, selecting the 1000 most variant genes (genes with higher standard ...
4
votes
2answers
67 views

Relative microRNA comparison from from TCGA data?

I have a conceptual question that I was hoping someone could answer. Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after ...
2
votes
2answers
625 views

TCGA gene expression data are missing matched normal

I'm trying to use the TCGA data portal to get gene expression data for cancer tissues, but I'm not sure what "Tumor matched normal" means. It is unclear to me if the values are already compared to a ...
4
votes
2answers
296 views

How can I text-mine full-text articles from PubMed? [closed]

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 ...
3
votes
0answers
30 views

Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
-2
votes
1answer
51 views

What makes a good phylogenetic tree?

How can one improve a phylogenetic tree? If one was to make the 'golden standard' of phylogenetic trees what features would it have? Would it be highly reliable, well resolved etc? What other features ...
0
votes
0answers
35 views

Best software for protein in electric field modeling?

I'm trying to find a free, or cheap, software program to model the movement of a heterotrimeric protein in an alternating electric field. The dipole and crystal structure of the trimer are known. ...
1
vote
1answer
28 views
1
vote
0answers
37 views

Common Metrics of Assessing DNA Sequence Quality

What are commonly accepted metrics for assessing DNA sequence quality (platform-specific answers are fine)? I am relatively new to this topic, and I want to either find or code (in Python or C++) ...
1
vote
0answers
30 views

Compare Proteins - Structural / Sequence parameters

I have been working on algorithms that extract co evolutionary signatures from protein sequence. As a result of my work I got some evolutionary information which possibly explains cotranslational ...
0
votes
0answers
24 views
2
votes
2answers
97 views

Core Biological concepts explained to a Computer Scientist?

I am a computer scientist delving into Bioinformatics and I need to gain insight in biological phenomena. How would you explain three core concepts as: Evolution, Selection and Variation, to a ...
4
votes
1answer
27 views

Epistasis Across Chromosomes and Individuals 'Homozygous for Interactions'

Apologies for any failures in nomenclature. I'm a mathematician who is making a foray into genetics for a masters thesis. Specifically, I'm generating artificial diploid genetic sequence data and ...
4
votes
1answer
60 views

Where to find E.coli gene expression data?

I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc. I have ...