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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106 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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50 views

How can I download a gene sequence from GenBank (NCBI)? [closed]

Could you tell me the steps to find and download a gene sequence from GeneBank? I would appreciate your help.
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105 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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59 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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83 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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66 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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42 views

What are pseudoknots?

I'm trying to get my head around what a pseudoknot is and how I can identify them given some RNA string. For example, suppose I have a string s = CGUUGUGUACACGAUAGUACAU. Suppose the two longest ...
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80 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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252 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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135 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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526 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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37 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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98 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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63 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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184 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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92 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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134 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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45 views

What is the difference between gene and CDS annotations?

I have a bunch of sequence files fetched from the EBI ENA and I'm trying to find the end of the 5' UTR for specific genes. The UTR itself doesn't seem to be annotated in most sequence files I have. ...
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65 views

Aligning multiple sequences in heterogeneous group

I have a list of ~200 DNA sequences, representing probably 50 different genomic regions but they're all mixed up. For example, if I have seq1, seq2.... seq10, ...
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60 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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29 views

PDB file SEQRES have different datas?

In PDB file, SEQRES represent the aminoacids but some pdb file present the "GLC" and some other. for example ...
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79 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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101 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
51 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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276 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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59 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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152 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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262 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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126 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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148 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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734 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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17 views

RNA-Polymerase III transcribed genes

I have a list of differentially regulated genes from a high-throughput experiment of the human genome. I would like to find out which of these genes are transcribed by a RNA polymerase III and which ...
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70 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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51 views

How do you convert mtDNA sequences in FASTA to FSTAT format?

I've got control region sequence data from a population of shark and I'm looking to convert this from FASTA to FSTAT in order to calculated the effective population size of females. The software I ...
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43 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 ...
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80 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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57 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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120 views

Distance matrix with different length sequences

In a project we're doing (in python), we want to create a distance matrix for a phylogenetic tree with multiple, different length sequences. However, what we've seen so far (AlignIO in biopython, ...
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1answer
57 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 ...
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1answer
21 views

Microarray probe and target

In a microarray, which one is called a target and which one is the probe? the one that is added later , is that the probe or the one present in the slots of the microarray, that is the probe? (I have ...
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1answer
50 views

Applying Constraint Programming to sequence alignment/analysis

My Masters program is focused on formal methods such as SAT solving and constraint programming. I am interested in applying such techniques to problems in sequence alignment and sequence analysis, ...
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141 views

Convert gene name to uniprot ID

i have a list of gene name in a file CHRNB2 EGR2 GCK KRT14 LMNA FGF3 TK2 ABCC8 How can I map them to uniprot ID ? P.S I tried Uniprot "ID mapping" ...
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111 views

Heterochromatin binding sites position information

I am working on a project and I'm trying to find data on the position of genes and heterochromatin binding sites such as HP1 in Drosophila melanogaster. Is this information available for the DGRP ...
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1answer
41 views

Alleles notation in SNPPedia criteria

I can understand the allele notation when is in the form rs8176719(T;T) or rs8176719(G) but recently i found this ones rs8176719(T;-) or rs8176719(-;T). So im confused, rs8176719(T;-) is the same as ...
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29 views

Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?

Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an ...
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1answer
66 views

downloading a reference genome for alignment

I am currently working through the code example on the MATLAB website. It requires me to download the reference genome of Arabidopsis thaliana (thale cress) so I can use BowTie2 to align the Chip-Seq ...
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46 views

About the quality of microsatellites

I built a script to detect microsatellites in a FASTA file. However, there are thousands of possibilities. So, my question is: what are the markers of a "good" or "useful" microsatellite? - How ...
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49 views

What is the close and related genome used for in Gene models?

all I am a little bit confused about using the related genome or reference genome. When we have a reference genome, we can do alignment. Also we can do the assembly. Can you give some more reason ...
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34 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 ...
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72 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 ...