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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5
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4k views

What is the difference between local and global sequence alignments?

Obviously there are a bunch of different alignment tools out there, and I don't want to get bogged down in the maths behind them as this differs from software version to version. I am aware that ...
2
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1answer
129 views

How to determine the direction of regulation of a gene by comparing gene expressions?

I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a ...
0
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0answers
30 views

What is the suitable terminology to describe this study approach?

I need to know the correct term(s) which are usually used in the parlance of both biology and bioinformatics for this study approach: About 11 transcripts were investigated using qPCR for a number of ...
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2answers
282 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 ...
2
votes
1answer
43 views

H O N C alternatives for organic life?

Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures. Are there ...
5
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1answer
79 views

Base Substitution Probabilities Derivation

In Felsenstein's 1981 Paper Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach, he describes (in equations (6) and (7)) a derivation of the equation of the probability of a ...
0
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1answer
87 views

Color van der waals bonds in swiss PdbViewer

I'm trying to color certain amino acid's van der waals bonds as in the following picture: can anybody please describe the steps to accomplish that?
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2answers
82 views

Gene perturbation, what is it used for, explain to computer scientists? [closed]

I am trying to build a gene regulation network, and I need some basic knowledge of it. So, in gene research, we perturb genes. Such as knock down them? Can people tell 2 or 3 experiment methods to ...
7
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3answers
131 views

What is the potential function of ultra-conserved elements in the genome?

If selection pressure results in conservation of DNA sequences, what is the most plausible explanation for the existence of ultra-conserved elements (refs here and here) given that there hasn't been ...
1
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0answers
43 views

Infering the statistical tests performed in a paper [closed]

I am in great need of help in order to infer the statistical hypothesis tests performed in this paper (Xanthelasmata, arcus corneae, and ischaemic vascular disease and death in general population: ...
2
votes
1answer
98 views

Biological meaning/interpretation of clustering coefficience

I have been looking for some time to find an answer to the following question. I would be grateful for any help/advice or directions. I work very frequently with large number of proteins and assess ...
0
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1answer
57 views

Needing help in order to infer the statistical hypothesis tests performed in an old paper

I am in great need of help in order to infer the statistical hypothesis tests performed in an old paper. However I need to make some reasonable guesses only from the abstract of the paper since the ...
0
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2answers
136 views

How do download a list of the gene length of all genes?

I would like to get the gene length information of all the human genes. Is there a quick way to get this information? Thank you!
2
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2answers
115 views

Image analysis of GFP-tagged protein localization bursts

I'm reading an article (full text here) that analyze the dynamics of localization of a GFP-tagged transcription factor (Crz1) over the time at the single-cell level, by taking movies in a fluorescent ...
1
vote
1answer
63 views

Plastid and mitochondria

I am not biologist, so please bear with me for this basic question. Although I tried googling, I am confused. What is difference between plastid, chloroplast and mitochondria? Are there any plant ...
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2answers
221 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 ...
1
vote
2answers
97 views

How do you find pre-miRNAs from mature miRNA Blast output?

So in short, I did a blastn with standalone blast using all known miRNAs against the EST sequences in a genome (word length 7 and e-value 0.01). Now to confirm one of the next steps would be obtain ...
5
votes
2answers
156 views

introduction to Chip Seq

I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've ...
0
votes
1answer
22 views

How do I share a protocol on Synbiota? [closed]

After I create a protocol on Synbiota, how can I share it with colleagues not in my project?
2
votes
1answer
43 views

Number of autoregulation and FFL motifs in a network

Suppose we have a network with N* nodes (N* is the number of internal nodes). Every directed link in this network exists with probability p. What would be the number of: motifs that are ...
1
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2answers
54 views

Which types of hydrogen bonds are known to exist in RNA secondary structures?

I'm programming an implementation of an algorithm for pattern matching in RNA structures. The algorithm assumes the following types of base pairs: Plain: No base pairs (just the primary structure of ...
0
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0answers
28 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 ...
0
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0answers
51 views

Width of vein in finger

I am working on my bachelors thesis, where one part of it is to find width of vein in fingertip. I use database images and extract vein patterns from it, but i have to calculate the width of vein and ...
2
votes
1answer
163 views

ChIP-seq and the output of SPP

I have been processing some ChIP-seq data with the R package spp. I looked through the literature (ENCODE uses it) and it seemed that spp is indicated as a good program to use. I have found and ...
2
votes
1answer
59 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
54 views

Bioinformatics : Drawbacks of using ORA(Overlap Analysis)

What do you think are the potential drawbacks/weakness of using ORA to explain distinction between two phenotypes. I identified a few which were the dependencies of DE and the statistical method used ...
6
votes
1answer
117 views

How can promoter binding sites be determined?

I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it ...
3
votes
1answer
53 views

relative-rate of evolution

I am supposed to calculate the relative rate of evolution of two sequences (human and sheep) with a chicken serving as the outgroup. The sequences are pretty long, so I will just create a short ...
4
votes
2answers
86 views

GO terms for non-model organisms

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have ...
1
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1answer
32 views

Single channel micro arrays

What does single channel microarray mean? When is it used? Thank you for your case in advance.
0
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0answers
52 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 ...
2
votes
1answer
236 views

How to check if a fastq file has single or paired end reads

I am trying to check if a fastq file has single or paired end reads. How can I achieve this with an error-proof method? I checked wikipedia and MAQ but I want to know if is there a reliable document ...
1
vote
1answer
45 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 ...
0
votes
1answer
69 views

Systems Biology of triacylglycerol (TAG) synthesis in Jatropha

I need the genetic regulatory network of TAG synthesis (Kennedy pathway) of Jatropha plant?? Or is there any way to convert metabolic pathway into genetic regulatory network?
1
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2answers
83 views

what does sequences overlap indicate

what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other and how does one go on to ...
1
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3answers
55 views

Using PSI-BLAST

I understand that the first BLAST yields almost the same results as blastp. The second time the iterated blast generates different results as it uses different matrix based on our first result. But I ...
1
vote
1answer
56 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 ...
-3
votes
1answer
50 views

Biopython error [closed]

from Bio import SeqIO for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"): ... print(seq_record.id) File "", line 2 print(seq_record.id) ...
2
votes
1answer
229 views

basic programming and bioinformatics [closed]

As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work ...
0
votes
3answers
85 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
0
votes
0answers
35 views

comparing conventional phylogenetic tree to phylogenetic trees which are based on enzymes

I built trees (for 4 organisms: mouse, human, drosophila and C-elegans) for different enzymes family, compared them to the conventional tree, and try to explain them. how would you explain these ...
4
votes
3answers
150 views

Why do we need deep sequencing?

Why do we need deep sequencing? Why cannot the sequencing technologies read all the nucleotides correctly at the first read? Sorry since this question is too trivial, I don't have a biological ...
4
votes
2answers
105 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 ...
2
votes
2answers
39 views

RNA secondary structure comparison

Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common ...
3
votes
1answer
631 views

RNA-seq analysis - q-values in cuffdiff

I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change ...
1
vote
1answer
72 views

Transcribing DNA to mRNA with introns

I have a problem in my bioinformatics class that I thought I was doing right, but someone else is getting a different answer. Here is the problem: Given the following DNA sequence, ...
2
votes
2answers
54 views

Connection between genes and pathways

I am reading about a paper about inferencing pathway information in cancer cells. Authors refer to ERBB2 as a gene and a pathway. I don't have solid biology background. What exactly means when we ...
2
votes
1answer
99 views

Transition/Transversion ratio

I'm taking a bioinformatics class and at this point we are just going over basic stuff about molecular biology. Half of the class is doing reading/research on our own, so there isn't much class time ...
4
votes
1answer
52 views

Where can I find histograms and tables of prevalence of mutations in cancer?

At some point in the past I found a cancer portal site which had aggregated data for the relationships between various mutations and their prevalence in cancer types and tumor data. The data was ...
4
votes
2answers
81 views

Reference sequence for defining single nucleotide polymorphisms

Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in ("dbSNP—Database for Single ...