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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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
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1answer
73 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 ...
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1answer
79 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 ...
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2answers
137 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: ...
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0answers
91 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 ...
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0answers
40 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 ...
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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 ...
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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 ...
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2answers
517 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
189 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?
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2answers
104 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
234 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
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1answer
69 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 ...
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23 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....
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1answer
75 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 ...
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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 ...
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1answer
33 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
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1answer
269 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
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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 ...
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2answers
175 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
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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, ...
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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 ...
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1answer
42 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 ...
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2answers
523 views

What is the meaning of dots and dashes in clustalw?

I am converting outputs in stockholm format to clustalw using ...
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1answer
60 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?
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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?
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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
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1answer
40 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 ...
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2answers
94 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 ...
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2answers
958 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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1answer
56 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
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1answer
36 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 ...
2
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2answers
146 views

In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?

I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis. I also understand cloning can be a ...
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0answers
30 views

How to find gene variation in NCBI?

I am looking for variations of my gene so that I can design a primer. But, I do not know how to found the relative links in NCBI. Where can I start?
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2answers
109 views

How to use swiss-mod to predict the secondary structure and 3D structure of a protein?

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, ...
2
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2answers
268 views

GATK workflow for Cancer

I am just starting to learn to use bioinformatics tools. My university has a limited and expensive bioinformatics team, so I'm mostly on my own except for big questions. I am planning to use GATK to ...
3
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1answer
172 views

How to perform a DNA structural alignment in pymol

How can I "fit" two DNA structures having different nucleotide sequences in pymol? I would like to use the structure of a DNA binding protein in pdb (1h9t), which is bound to DNA in the pdb file, ...
11
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2answers
238 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 ...
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0answers
43 views

Running (standalone) PSI-BLAST Against Multiple Queries

I'm new in standalone blast+ and in linux terminal. I set the bash-profile to load the PATH and BLASTDB for my blast already, but I don't know how to use psi-blast yet. How can I do the search ...
0
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1answer
632 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 ...
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3answers
40 views

importance of cDNA sequencing of a specific gene in different plants

i want to know what if i made a sequence of cDNA of a specific gene in different plants - what is the important from the sequence and can if found difference between plants , and can i use this ...
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0answers
32 views

Biological modeling languages - some basic issues

I am trying to get used to with couple of modeling languages in biological context like SBML, BioPAX, Kappa and BEL. Some basic issues came up to my mind that are unclear to me even after a lot of ...
0
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1answer
102 views

How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis

I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be ...
2
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1answer
48 views

In DNA sequencing, is “mate pairs” synonymous with “paired ends”? If not, how do they differ?

By just looking at Roach et al's paper I get the impression that they are the same thing, and the Wikipedia URL for the former is a redirect to the latter. However, I suspect they are not exactly the ...
2
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2answers
48 views

How does one find the corresponding SNPs in the pair of chromonosmes in a FASTA file?

You might say I'm an amateur bioinformatician, or trying to become one. I have a BAM file, from which I have succeeded, using UGENE , in extracting consensus data in FASTA format. I now see a single ...
8
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8answers
624 views

Are there examples of encryption in nature?

There are examples of mathematics in nature such as Fibonacci number, fractals, etc. Are there examples of encrypted information? What I am looking for is a pattern that seems random on the ...
1
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1answer
34 views

Metrics or operations on genome sequences in human genomic research?

Edit distance may be an important metric for measuring the similarity of two genome sequences. For example, if A = GCAATT and B= CGAATA, then the edit distance of A and B is 3. Such a metric is ...
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1answer
46 views

How to Determine the Most Conserved Sequence from BLAST Result?

I used BLAST to find the best aligned DNA sequence to my query sequence. The BLAST result shows a number of sequences that it calculated to be the best aligned sequences to the query sequence that I ...
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1answer
58 views

How to annotate a .broadpeak file with 9 columns?

I have this peak file I retrieved from an ENCODE chip-seq matrix. Its .broadpeak file looks like this: ...
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1answer
64 views

Does a DNA sequence has its own derivation tree or pattern?

I am new to bioinformatics and natural language processing. In linguistics, they have Treebank - derivation/parse tree for each sentence. For example, a sentence "Sara sleeps" can be visualized by a ...