Tagged Questions

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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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: ...
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 ...
1
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2answers
168 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 ...
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1answer
57 views

Can someone suggest me good opencourseware links for learning computational biology basics?

My internet is slow and I have only 1GB data usage allowed for this month. And I want to make maximum out of it for learning some basics of computational biology. Which are the best online course ...
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2answers
166 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!
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2answers
121 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)?
3
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1answer
110 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 ...
4
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3answers
108 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
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2answers
88 views

chimeric sequences [closed]

I understand that chimeric sequence identification is done in results of sequencing projects to remove them and improve the quality of the output. I am unsure as to how they show up during sequencing. ...
2
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2answers
81 views

Sequence alignment scoring

The following table is from Deonier's text Computational Gene Analysis at p. 152. This is an exercise in global sequence alignment and scoring of alternative sequences. The text proposed a solution ...
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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?
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2answers
57 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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2answers
59 views

is there a way to do batch download for all gene pathways?

I would like to download all the gene pathways and genes of each pathway. Preferably, gene length of each gene as well. It would be a lot more convenient if there is an R package.
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0answers
53 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 ...
5
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2answers
179 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 ...
7
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1answer
218 views

List of np-hard problems in biology/bioinformatics

I'm not sure if this is the right place for this but... I am looking for a list of computationally "hard" problems such that if a problem from this list could be solved effectively, it would be ...
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2answers
352 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 ...
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 ...
2
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1answer
44 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 ...
4
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1answer
55 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 ...
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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1answer
75 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 ...
1
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1answer
33 views

Single channel micro arrays

What does single channel microarray mean? When is it used? Thank you for your case in advance.
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0answers
59 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 ...
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3answers
81 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 ...
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1answer
46 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 ...
2
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2answers
70 views

Databases for metabolic pathways of human disease

Which databases contain the metabolic pathway of human diseases? I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.
0
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1answer
70 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?
2
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1answer
272 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 ...
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3answers
57 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
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1answer
61 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 ...
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1answer
52 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) ...
6
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1answer
130 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 ...
2
votes
1answer
265 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
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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 ...
1
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1answer
56 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 ...
0
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3answers
87 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
1
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2answers
111 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 ...
2
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2answers
58 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 ...
4
votes
2answers
113 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 ...
4
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2answers
97 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 ...
2
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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 ...
1
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1answer
74 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
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1answer
102 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 ...
2
votes
2answers
56 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 ...
4
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2answers
82 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 ...
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 ...
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3answers
67 views

What is the datatype of dna sample?

What is the type of data you get when analyzing dna of a person? If you want to store them in a database, what type of field you will need (text,number,hex)? And what should be it's length?
1
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1answer
160 views

Codon alignment via Python? [closed]

I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process. So far.. I retrive pairs of orthologous DNA sequences from ...