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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5answers
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Why did high A+T content create problems for the Plasmodium falciparum genome project?

The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
5
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1answer
95 views

Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
0
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1answer
60 views

results of FgenesH and GenScan

Why FgenesH and Genscan don't give good results as I have prdicted number of genes of Chromosome 16 which according to NCBI are 86 but the results I have obtained are 57 genes predicted by FgenesH and ...
0
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0answers
18 views

Looking for hard cell segmentation problem

I am a physicist working on a new image segmentation technique, and I would like to test it by segmenting some images with low-refined cells on a noisy background... Do you know where I could find ...
0
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0answers
7 views

Oligomeric states of Phyre model

Is it possible to generate an oligomeric state for a phyre model? As it lacks crystal packing information "Generate>Symmetry_mates" obviously does not work in PyMol. I assume that the fit is not ...
3
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2answers
128 views

Construct Phylogeny form Edgelist

I am working on large scale biodiversity simulations and have collected a lot of data on simulated phylogenies. I have a list of child-parent edgelist species in the form: ...
1
vote
2answers
54 views

How is e-value calculated in BLAST 2 sequences (BLAST+)?

In the BLAST+ packages, you can align two sequences instead of searching a database: tblastn -query seq1.fa -subject seq1.fa The web BLAST documentation states ...
4
votes
1answer
50 views

What does “~mitochondrial DNA ~bp linear DNA” means?

I'm surfing NCBI website -Nucleotide- to find some examples of real DNA sequences to use in my small homework project. My question is related to the title of a DNA sequence below: Sus scrofa ...
0
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0answers
20 views

NMDS analysis - weird plots

I ran a NMDS analysis on 16S tag sequencing data on three different 16S regions, and would like to establish the regression coefficients (R, p) from this. All the data is stored within a combination ...
4
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1answer
66 views

Question about SAM CIGAR string

My question is about the CIGAR specification. The documentation states: M 0 alignment match (can be a sequence match or mismatch) ...
1
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2answers
49 views

identifying which SNPs sit in TFBS (Yeast)

i have a set of ~11k SNPs for Saccharomyces cerevisiae, baker's yeast and i would like to identify which ones of these sit in transcription factor binding sites and if they do information on the ...
1
vote
1answer
63 views

From STRUCTURE to FSTAT format

From numerical simulations I output a file that is input to STRUCTURE (Hubisz et al. 2009). I now realize that I would need to process my data with FSTAT (Goudet 1995). Both are text files. Is there ...
0
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0answers
11 views

Where to Find Pedigree-Linkage Data for Computational Pedigree Analysis

I'm currently working on a project that uses graphical models (Bayesian networks) for pedigree analysis. My group developed a few models several months ago, but the original data used to develop the ...
0
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0answers
46 views

Interpreting soft clipping in a SAM alignment

I am interpreting CAGE data. I have noticed that in the SAM files I am analysing, there are many pairs of lines of the form (e.g.) ...
1
vote
1answer
90 views

What are the basic skills required to pursue future studies in theoretical ecology? [closed]

I am a student and just about to choose a project for my Master's thesis in biology. I want to pursue studies in theoretical ecology in the future. Between field ecology and computational biology (as ...
0
votes
1answer
18 views

what is the principle behind Allele Frequency Net Database

I just wanted to know what is the basic principle of Allele*Frequency Net Database. How are the frequencies present in them calculated??
1
vote
1answer
122 views

how to change format of ent file into PDB format?

whenever i download files from Protein Data Bank(PDB),they are downloaded in .ent format. How can i convert them into PDB format??
1
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0answers
11 views

Where can one find completed and processed Hi-C datasets?

I and a statistics graduate student at UCR, and I am working on Optimal Binning schemes and peak detection in Hi-C data analysis (a dataset that conveys information about proximity of a DNA strand ...
0
votes
1answer
78 views

BLAST(Basic Local Alignment Search Tool) is heuristic?

How can we say that BLAST is based on a heuristic algorithm, as after finding one common word in the query sequence and a database sequence it performs pairwise alignment by dynamic programming - ...
2
votes
1answer
77 views

What are some useful (starter) metrics to use on phylogenetic trees?

Im doing a computational biology project in which I simulate evolution under different inheritance rulesets and I am generating phylogenetic trees (beautifully visualised in python with ete3, which I ...
1
vote
1answer
93 views

Where can I find FDist2 executable?

I am trying to download the program FDist2 (Beaumont and Nichols 1996) for Mac but for some reason it appears that all the links I find are broken. It appears that the program Lositan is an faster ...
6
votes
2answers
160 views

Why is the quality range of fastq format so broad?

Referring to fastq format, it is clear that in fastq format, there are 94 quality value for a sequenced Nucleic Acid of a DNA sequence read and they are: ...
9
votes
0answers
101 views

Standard practice for generating rarefaction curves from Next Generation Sequencing data

We have a few million 18S reads from a particular environment. The reads have been clustered into Operational Taxonomic Unit (OTU), and the OTUs annotated against a reference database. To generate a ...
2
votes
0answers
41 views

How to predict cancer-related proteins in Protein-Protein Interaction networks [closed]

Protein-Protein Interaction networks are known. It's an undirected graph. Each row of the networks is like this (Protein 2 - Protein 6), and It represents the interaction between Protein 2 and Protein ...
5
votes
2answers
1k views

What are we missing about the real workings of the evolutionary process? [closed]

As a scientist (and a computer scientist at that) my view is that if we cannot simulate a process we have not understood it properly. I have been following the interesting field of Artificial Life for ...
0
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1answer
44 views

Which secondary structures of RNA are symmetric? [closed]

I'm trying to understand what is the meaning of this statement. A088518 Symmetric secondary structures of RNA molecules with n nucleotides. 4 %I %S ...
2
votes
2answers
534 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 ...
4
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2answers
190 views

Basic Local Alignment Search Tool (BLAST)

Why would BLASTP (Basic Local Alignment Search Tool) be a poor tool to search for motifs in protein sequences?
2
votes
2answers
106 views

TFBS predictions for yeast and pombe?

Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like ...
11
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2answers
235 views

Is there a program that simulates biology on a molecular level?

Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?
2
votes
1answer
71 views

Is there a free software for manual sequence annotation?

I'm looking for a software that would allow me to make a quick graphical annotation of the structural features of a sequence. Something that would look like what you get in jalview, with your sequence ...
1
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0answers
24 views

Degenerate primer designing software

Can any one provide online free degenerate primer designing software. I have tried couple of them like CODEHOP is one where BLOCK formatting step finding difficulty, can anyone help me out....
0
votes
1answer
77 views

Does increasing the value of k in k-fold coverage requires more memory?

Study: Here is what is k-fold coverage which is know as sequence coverage. According to this, 2-fold coverage means the whole DNA is sequenced more twice in average. Question: If I have a genome ...
1
vote
1answer
61 views

Do the BLAST scores have any relation between them?

Is there any relation among the BLAST scores (E-value, similarity, identity, gap, bit score)? Is the e-value score for an alignment proportional to other scores, such as similarity score (i.e. the ...
0
votes
1answer
34 views

Why does uniprot sometimes not label single-pass transmembrane proteins as “anchors”?

Currently, section 3a) of unitprot TRANSMEM reference page divides single-pass transmembrane proteins into 4 types: ...
3
votes
1answer
277 views

Software to calculate Fst from sequence data

I'm looking for a software to calculate Fst from 3 loci DNA data of individuals from a metapopulation. I don't have any prior on the population structure (have no idea of the number of subpopulations ...
0
votes
1answer
55 views

Expected dS/dN ratio for exome

I am trying to determine whether or not my sequencing data has more/less non-synonymous mutations than would be expected. My understanding is that there is some fixed ds/dn ratio for the human exome ...
5
votes
2answers
185 views

Where can I find mutation datasets for cancer?

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 ...
5
votes
1answer
84 views

How many genes does D. melanogaster have?

Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, ...
4
votes
2answers
66 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 ...
1
vote
1answer
45 views

What does uniprot consider “unambiguous” evidence for the subcellular domain of a protein?

Uniprot has annotation for subcellular location of protein domains. This topological domain information of proteins is under the TOPO_DOM flag. In most cases the ...
2
votes
2answers
567 views

What is the meaning of dots and dashes in clustalw?

I am converting outputs in stockholm format to clustalw using ...
1
vote
1answer
61 views

How is the probability of a sequence occuring with BLAST calculated?

What is the probability that a given nucleotide/amino acid sequence will occur in the whole database program BLAST searches in? How this probability is calculated?
0
votes
0answers
33 views

Is it possible to have raw ngs data to practice

I'm looking for raw human ngs data to practice in bioinformatics. Better if it is from different machines (illumina, roche, pacsbio, etc). Panels, exomes and genomes. Anyone knows something?
3
votes
2answers
83 views

Microbiome Data

How is it possible to access microbiome data like that found here? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the Human Biome Project. Thanks for any ...
2
votes
1answer
42 views

How to find conserved residues across species?

I want to identify if certain phosphorylation sites are conserved for protein X across humans and yeast. I know from MS data that there are 4 phosphorylation sites in Human protein X. In order to ...
2
votes
2answers
105 views

How to build a trimeric protein structure from monomeric PDB file?

Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full ...
2
votes
2answers
1k 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!
-1
votes
1answer
57 views

Difference between various evolutionary terms [closed]

Could someone kindly explain me the difference between Phylogeny, Phylogenetic Tree, Evolutionary Trees, Phylotype, Clusters, OTU (Open Taxonomic Units). Or if possible please do suggest me a ...
1
vote
1answer
37 views

gene transformation from plant to plant - transgenic plant

I want to know if the expression of a transfered gene depends on source of the gene, if e.g.: 1] I isolate a gene from plant and transfered it to the same plant? 2] I isolate a gene that is highly ...