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 can I create R8 (homopolymer repeat) filter without using illumina pipeline?

illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and ...
3
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0answers
182 views

How to get only perfect matches with blastn? [closed]

I have installed Blast locally and I've configured the nucleotide database to use. I want to search some sequences (from a .fastafile) in this genome. So I used blastn: ...
3
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0answers
51 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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293 views

Accuracy of genome size estimation by flow cytometry

I'm working on a genome project and using an in silico k-mer analysis to estimate the size of our genome based on the available Illumina reads. The k-mer based estimate is consistent across a wide ...
3
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0answers
140 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 ...
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6answers
165 views

Which information can be obtained from a list of gene names?

Lets say I only have a list of gene names. I know they are up regulated and I know they are related to cancer. What information can I obtain from having only the names of genes? For example is there ...
2
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3answers
212 views

fastq-dump using mkfifo to stream data

So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk. I'm curious whether ...
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2answers
87 views

peptide MHC microarray

"The recent technology is peptide–MHC microarray or artificial antigen-presenting chip. In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a surface,...
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2answers
104 views

Consensus codon optimization by organism

Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables ...
2
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1answer
79 views

Programs/software to graph biological data [closed]

I am curious about what sort of programs people in my field of academia are using to graph their data. I am a master student in biochemistry, and have more or less only used excel (on rare occasions I ...
2
votes
1answer
366 views

Bowtie: cannot read fasta file?

I am trying to use bowtie2 to analyze my data in FASTA format, but it seems that this version can't read properly my data. My command line is as follows: ...
2
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2answers
64 views

Simulating Drug Entry in Protein and binding?

Is there any simulation protocol or paper which can simulate the dynamics of drug entry and interaction with the target protein?
2
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1answer
384 views

Plastid and mitochondria

I am not a biologist, so please bear with me for this basic question. Although I tried googling, I am confused. What is the difference between plastids, chloroplasts and mitochondria? Are there any ...
2
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3answers
155 views

What is happening in each iteration of 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 ...
2
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1answer
112 views

How to build S16 rRNAs phylogenetic trees?

Here is what I know so far: Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al.[1] it is enough to select the most similar ones. There are stem regions in the ...
2
votes
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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3answers
727 views

What is the biological significance of finding palindromes in DNA sequence?

I found a function called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of ...
2
votes
1answer
75 views

How do I find the number of child terms associated with a specific GO term?

I am trying to figure out how to find the number of child terms associated with a specific Gene Ontology (GO) term using QuickGO, without just counting the amount of terms in a list. For example when ...
2
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2answers
119 views

Can all biological processes be understood as computations and studied as such? [closed]

Can we understand a cell as an organic computational device? In that case the whole organism can be considered an ensemble of a large number of interacting computational devices? If this is the case,...
2
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2answers
205 views

How to retrieve full gene names list and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any)?

How to retrieve full gene names and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any other software or language)? Is it possible vice versa: having full gene ...
2
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2answers
125 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 ...
2
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2answers
731 views

MOL2 to PDBQT conversion via OpenBabel and MGLTools removes hydrogen atoms

I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms ...
2
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2answers
62 views

RNA secondary structure comparison

Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common ...
2
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1answer
138 views

Expanding the SETI initiative to seek intelligent data within DNA sequences?

I've recently read a couple articles dealing with long term data storage, and DNA was suggested as one of the prime candidates for long term storage of digital data additionally, there is this article ...
2
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2answers
226 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 ...
2
votes
1answer
36 views

Why my base-quality in alignment is not perfect?

I have a fasta file with some DNA sequences. I would like to simulate next-generation sequencing reads from it. I'm doing it without any base error and mutation error. ...
2
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1answer
74 views

Are there journals for theoretical models of protein-protein interactions?

Are there respectable scientific journals for publishing models of protein-protein interactions obtained by docking simulations? I would also discuss the biological significance of the particular mode ...
2
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2answers
374 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 ...
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2answers
1k 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!
2
votes
2answers
75 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 ...
2
votes
2answers
1k 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 ...
2
votes
1answer
1k views

What do rs id, allele coded 0 and allele coded 1 mean?

So, for a project I've been working on (different story), I've been looking at the HapMap Project, and their free online files. In their README file, they talk about how for each legend file for each ...
2
votes
2answers
107 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 ...
2
votes
3answers
79 views

DNA to Binary Distance Computation [closed]

If I represent DNA as binary values, what is the best way of computing distance between them. So : A = 00, T = 11, G = 01 and C = 10 Hamming Distance between ATGC and TAAC is 3, however their ...
2
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2answers
126 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 ...
2
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2answers
114 views

Core Biological concepts explained to a Computer Scientist?

I am a computer scientist delving into Bioinformatics and I need to gain insight in biological phenomena. How would you explain three core concepts as: Evolution, Selection and Variation, to a ...
2
votes
1answer
85 views

Protein PTM site prediction

Is there any in silico analysis method to predict post-translational modification sites on a given protein?
2
votes
1answer
33 views

What are host cellular factors?

With respect to this paper: Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication What does the term "host cellular factors" mean??
2
votes
1answer
128 views

Whole genome sequence analysis software

Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, ...
2
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2answers
106 views

Downloading specific yeast genes in an automated manner?

I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, ...
2
votes
1answer
54 views

Data Bias in protein-protein interactions data

Databases like STRING have so many predicted as well as experimental interactions data for many organisms.However there is a bias in the data which they have?. a)The first is gene co-occurrence ...
2
votes
2answers
206 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 ...
2
votes
2answers
565 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 ...
2
votes
1answer
109 views

H O N C alternatives for organic life?

Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures. Are there ...
2
votes
2answers
138 views

chimeric sequences [closed]

I understand that chimeric sequence identification is done in results of sequencing projects to remove them and improve the quality of the output. I am unsure as to how they show up during sequencing. ...
2
votes
1answer
69 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 ...
2
votes
2answers
70 views

Connection between genes and pathways

I am reading about a paper about inferencing pathway information in cancer cells. Authors refer to ERBB2 as a gene and a pathway. I don't have solid biology background. What exactly means when we ...
2
votes
2answers
2k views

Primer design for Gibson assembly

I'm trying to design a primer for Gibson assembly. My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid. I am unsure how to design my primers for ...
2
votes
3answers
132 views

What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?

I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
2
votes
1answer
94 views

Confusion related to a term probe-by-background interaction

I was reading a paper related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, ...