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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how to visualise a network of proteins complex? [closed]

I would like to know how to visualise a complex of several proteins lets say I have a list of proteins ...
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98 views

How can I make a protein interaction/protein-complex network?

Let's say I have a list of proteins ID. I would like to know whether I can find any complex based on that list. Any example, explanation is appreciated. An example input is what you see below. What ...
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60 views

Understanding common identifier codes (IDs) in biology databases

I know this is very basic but I would like to understand it and it's difficult to know where to begin with a new database. I have the output: ...
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How many residues can a reliable ab initio structural model contain?

A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be ...
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2answers
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What are sources for learning bioinformatics for self-learning?

What are the sources for learning bioinformatics(books, websites/MOOCs)? Does it require prior knowledge of programming language because I am a complete noob when it comes to programming language.
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Choice of Molecular markers to carry out molecular phylogenetics

For evolutionary analysis of different individuals within a population, the preferable molecular markers are non-coding regions of mitochondrial DNA. My question is that why they are used what is the ...
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1answer
52 views

Protein-protein interactions search

I used STRING db in order to find all the interactions of the precursor protein APP. What I specifically need is a confirmation (supported by some article and experiments in it). But significant ...
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1answer
73 views

In molecular docking, what is the difference between ligand and cofactor? [closed]

In molecular docking aspect, what is the difference between the Ligand and Cofactor? Can a Cofactor be used like a ligand for docking with the target?
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1answer
58 views

Predicting 3D structure of a protein?

While predicting 3D structure of a protein through homology modeling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
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1answer
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Prediction of transmembrane beta barrels?

I studied that prediction of transmembrane alpha helices is more easy and accurate and also good algorithms are available for their prediction. But when we move towards prediction of transmembrane ...
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1answer
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Where can I find SSR and/or SNPs that locate RC1 genes in Soybean? [closed]

Where should I look to find SSR and/or SNPs that locate RC1 genes in Soybean?
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1answer
161 views

Why is ab initio protein secondary structure prediction less reliable than alternatives?

To predict secondary structure of proteins three types of Algorithms are used Ab initio, homology based and neural networks. Among these neural networks prove to be more accurate and give good results ...
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1answer
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Obtaining a mapping of RefSeq ACs to Uniprot ACs

I am trying to obtain a mapping for RefSeq Accession Numbers to Uniprot Accession Numbers. I can write a script to do this for a list of RefSeq ACs like this: ...
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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 ...
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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 ...
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1answer
47 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 ...
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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 ...
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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 ...
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1answer
61 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) ...
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3answers
35 views

Identifiying a conserved residue in multiple PDB structures

I have a few hundred PDB structures of the same protein, and I need to identify a specific conserved residue in all of them. Originally I wanted to extract the sequences from the PDB files with ...
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1answer
35 views

BWA-MEM single strand or doublestrand alignment

In whole genome secondary analysis does BWA-MEM use a double stranded fasta reference or are reads aligned to only one, single stranded fasta reference?
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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 ...
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1answer
79 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 ...
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45 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.) ...
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1answer
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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??
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1answer
67 views

How can I find the most studied SNP of a gene?

How can I find the most studied SNP of a gene and diseases that the most studied SNP has been related to? I search in dbSNP database but I can't find it. What is the process?
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1answer
104 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??
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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 ...
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1answer
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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
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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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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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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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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
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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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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2answers
47 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 ...
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1answer
71 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 - ...
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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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1answer
92 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 ...
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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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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
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
70 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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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: ...
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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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1answer
56 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 ...
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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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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
97 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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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 ...