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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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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43 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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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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2answers
64 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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99 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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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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242 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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58 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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140 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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251 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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125 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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142 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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698 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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56 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
44 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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35 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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74 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
54 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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110 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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56 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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28 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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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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48 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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125 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
38 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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28 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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64 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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48 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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61 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 ...
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1answer
62 views

Hidden Markov Model

I read about the hidden markov model in bioinformatics. I amn't able to understand what it is. Can anyone explain me in brief and in very very simple words what it is ? I have NO background in ...
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2answers
273 views

Blast a sequence against multiple databases

I would like to BLASTP a list of protein sequences in fasta format against multiple protein databases. Since I'm only interested in the first hit of each database, it is possible that BLAST result ...
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1answer
78 views

(Web)app to search metabolic/signalling pathways

I'm looking for an application where you can find pathways by selecting a chemical occurring in it. So, for example, selecting 6-phosphogluconolactone brings up the pentose phosphate pathway or any ...
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1answer
49 views

Where can I find pdb files for macromolecules like receptors?

I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.
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1answer
61 views

Isoprenoid Diphosphate Concentration in Yeast saccharomyces cerevisiae

Isoprenoid Diphosphate(IPP) is an important metabolites which is precursor in lot of secondary metabolites like Dolichol diphosphate, ubiquinone, prenylated proteins and carotenoid (not synthesized ...
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1answer
92 views

Modeling yeast biochemical pathway using enzyme kinetics

I need enzyme concentration and metabolites concentration values to en-corporate these values in my model and do some simulation. I searched through some database yeast metabolome database ...
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1answer
68 views

Information Gene HBA2

Gene : HBA2? hemoglobin alpha 2 (Homo sapiens) I don't find any tissues (or organs) in which the expression of this gene is strongest? What is the size of the gene (promoter off) encoding this ...
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1answer
237 views

Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. The ssm is in the following format: ...
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1answer
96 views

Confusion related to the use of PCA to determine the background network

I was reading this paper related to use of gene expressions for predicting the drug response. I have this confusion, the paper has used PCA on the covariance matrix formed by the genes to get what is ...
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1answer
79 views

Recombination-based vs. Sequence-based genetic mapping

Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping? I think that in the past recombination-based ...
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1answer
36 views

Where can I find a transcriptome of a normal uveal melanocyte?

I am looking for a database where I could find a transcriptome (say obtained with a microarray analysis) of one (or ideally many) normal uveal melanocytes ?
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1answer
78 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 ...
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15 views

How do I use BEAST for divergence time estimation in this case?

I am interested in using BEAST to find the divergence time estimates of species separations within a genus of frogs. The genus separated from a outgroup taxon I have chosen around 80 million years ...
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2answers
50 views

Do variant callers miss rare variants in reference?

Generally variant calling programs (such as GATK-UnifiedGenotyper) look for differences between reference genome and submitted sequence. However, we all know that reference genome consist rare ...
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21 views

How to characterise a protein family in a putative genome island?

We have sequenced the genome of 200 bacterial strains belonging to the same species, a swine bacterial pathogen. In a previous work, it was observed that a protein family of adhesins is present in ...
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45 views

How to build gene interaction network based on correlation between gene expression values using software like Cytoscape and R?

How to build gene interaction network based on correlation between gene expression values using software like Cytoscape and R or smth else? I have .tab with gene names and total expression values. ...
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26 views

Download FunCat Database for Programmatic Access

I am enriching RNA-seq data for the fungus Neurospora crassa and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other ...