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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92 views

.Net DNA/Codon Parser

Does anyone know of an .NET (C#,VB.NET, maybe F#) DNA parser? If not I will probably make one, it doesn't seem like it would be hard. My general idea was to generate something that would report the ...
2
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1answer
436 views

Molecular Evolution: Mrbayes never stops?

When I use my own data to build Bayesian phylogenetic trees using the software Mrbayes, after many generations, it never reaches stopping status (namely, the average standard deviation of split ...
2
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241 views

How to calculate or know by experiment the entropy of enzymes or protein?

How do you calculate or experimentally determine the entropy of enzymes or protein? In particular, I am interested in Boltzmann and conformational entropy, and Gibbs free energy. Any references are ...
2
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1answer
407 views

Comparing BLAST and the Smith-Waterman algorithm

I've been asked: how does BLAST improve dynamic programming accuracy? I do know that BLAST is based on heuristic approach that approximates the Smith-Waterman algorithm and that the Smith-Waterman is ...
2
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1answer
199 views

How to learn DNA Origami

Can you tell me is there any good softwares and tutorials which can be used to learn DNA Origami. I am new to this and want to learn from basics. Advance thanks for your help edited: INSILICO
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1answer
60 views

what the best E-value cutoff in the miRNA homology search

I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop ...
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37 views

Biology Experiment Data (Hodgkin-Huxley)

I'm doing research into the Hodgkin-Huxley Model from an electronics/mathematics perspective and I'm looking to find actual numerical results from experiments on squid axons. I want to compare the ...
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29 views

Genome-wide methylation analysis: sources of technical error?

We are doing a genome-wide analysis of methylation via bisulfite sequencing for an insect species. Previous experimental techniques have suggested the presence of methylation in this organism, ...
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36 views

What does the term 'epitope mapping' mean? [closed]

Epitope mapping means identifying the binding site of antibodies on the target antigen. This means that the site to be identified is part of the antigen and not antibody, am I right?
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17 views

How are HSPs identified in UCLUST

I am new in Bioinformatics and recently studying UCLUST algorithm by Robert Edgar(2010). It is a fast sequence searching and clustering algorithm. The algorithm is heuristic based. I studied that ...
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0answers
49 views

Can a heterozygous allele show non-heterozygous expression in a family?

I'm doing a family study looking for novel cancer-associated variants in germ-line samples; the goal is to find candidate biomarkers which might be used for early detection. At an earlier step our ...
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101 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 ...
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33 views

dbSNP database table desciptions

I am trying to build a local implementation of dbSNP. I would like to know the descriptions of tables listed on ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606 and on ...
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43 views

Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?

E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms ...
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111 views

Good poly-A filtering rules or tools

I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have ...
2
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1answer
175 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 ...
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160 views

Too few transcripts from transcriptome assembler Oases

I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks. Here is my running command: ...
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0answers
253 views

Turn off multithreading in pymol [closed]

By default, pymol seems to grab the number of cores on the system for rendering. How can I force it to only use one core? Motivation: I have a large collection ...
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1answer
192 views

What is the difference between second and third generation sequencing

I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to ...
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1answer
93 views

Generating custom human DNA sequences based on traits such as eye colour?

I'm wondering if it would be possible to create software (unless some already exists, but I couldn't find any) to generate human DNA (the base pairs on the double helix) containing genes representing ...
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1answer
82 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
92 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 ...
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2answers
58 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 ...
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1answer
75 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, ...
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1answer
65 views

Is there a way to see what representations are currently displayed in PyMOL?

I am using PyMol to visualize .pdb protein structures. I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot ...
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2answers
66 views

Recommended sequence clustering algorithm for transcriptome data

I'm working on a project where I'm going to analyze a large amount of transcriptome data. After assembling our RNA-Seq reads into contigs using Trinity, it looks like I'm going to have about 10GB of ...
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2answers
186 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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122 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)?
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404 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 ...
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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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3answers
87 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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3answers
58 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 ...
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1answer
164 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 ...
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2answers
86 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 ...
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1answer
131 views

Chemical structure prediction

I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but are there any programs which will go from formula to structure ...
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1answer
36 views

Local BLAST Copy Number per Hit

I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at ...
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1answer
57 views

Modeling intracellular interactions between sender and receiver bacteria

I am involved in a modelling task of a biological process described as follows: -- "Objective: to model behavior of a sender receiver type system The process goes as follows Pre-signal [PS] is in ...
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2answers
44 views

Where to find the corrected BLOSUM matrices?

I was looking at this paper which talks about the miscalculations in the BLOSUM matrices and how the "wrong" BLOSUM62 matrix performs better than the corrected version. I was trying to find the ...
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1answer
90 views

Datasets of aligned nucleotide sequences [closed]

Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there? (I would like to use such datasets for training the alignment ...
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1answer
47 views

How to selectively download 3 fields from every record in UniProtKB?

I want to download a comprehensive table of protein names from uniprot.org. More precisely, I want to generate a tab-delimited table consisting of the id ...
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2answers
181 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

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 ...
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2answers
125 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 ...
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1answer
230 views

What are the differences between HPRD and BIOGRID databases?

What are the differences between HPRD and BIOGRID protein-protein interactions databases? What are their purposes? Why do we need two different databases? How is data collected into each one? How ...
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1answer
120 views

Single Nucleotide Polymorphisms and diseases

I am writing a report on how Single Nucleotide Polymorphisms occurring in each of these regions: Transcription factor (TF) binding sites Epigentic signals Splicing variants MicroRNA binding sites ...
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1answer
113 views

What are the characteristics of a promising drug target?

When researchers are looking to start developing a drug, what characteristics do they look for in the potential proteins (assuming they already have good quality structural models)?
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2answers
625 views

Batch convert miRNA names to Accession IDs?

Does anyone know of tools to convert lists of miR names to their miRBase Accession IDs? I know they exist, but my search keeps pulling up gene ID converters. EDIT: both @rg255 and @shigeta have ...
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2answers
62 views

What kind of technology is required for plant seed DNA printing? [closed]

I'm a programmer so I have little knowledge in the field of biology. However I have an interest in plants, GMOs and DNA (in terms of programming). So, I want to know what kind of technology is ...
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1answer
42 views

How can I compare the STRIDE and DSSP output files of a particular pdb file?

I have the pdb file of H-ras protein 5P21.pdb. I am supposed to compare the output of DSSP and STRIDE files after feeding this pdb file to respective servers. My question is how to make a quick ...
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1answer
49 views

BLASTn vs ORF tools

Sequencing projects sequence one strand and call that the + strand and then extrapolate the sequence of the - strand. This means that sometimes the genomic sequence that you download from a database ...