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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Finding diploid neanderthal alignment data, looking for ambiguity codes

I'm using Neanderthal alignment data from here: http://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html Specifically, the .bam files. I would like to find alignments for neanderthal ...
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14 views

This Sequence Data (DNA) has very few Methionin-starts. How is that possible?

I'm working on my first sequencing related project and I'm trying to find proteins with a specific PFAM ID (PF11999). The project is called "MMETSP", I searched the annotations for that ID, identified ...
18
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1answer
839 views

Additive genetic variance components from LMER in R

I've set up some dummy data in R which makes 40 genetically related lines, they are all siblings within a line so are genetically related by a factor of ½ thus additive genetic variance should be ...
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2answers
88 views

How to batch convert gene names to protein IDs in Uniprot?

I have a list of >1000 "ordered locus names" from the STRING database (also called gene numbers, ORF numbers, or CDS numbers by uniprot). They're in the form of 'b0014', 'b0015', etc. I'd like to ...
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0answers
9 views

Haploview command line: how to get tagSNP

I am trying to use Haploview command line software to compute haplotypes and extract tagSNP for those. When I use the standalone version on my local computer I tick the 'Show tags in blocks' option so ...
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25 views

generating grid around the protein

I am trying to generate a grid around my protein. Can you please help me with thatn ? I read your post saying it is possible to do that using PyRosetta. Can you please help me with that , how to do it ...
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1answer
35 views

“Other” classification for epitopes in the Immune Epitope Database (IEDB)

I used the immune epitope database (IEDB) to search for epitopes. I found some epitopes derived from antigens called " other" by IEDB. When I asked about it, the answer was "We use the "other" ...
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2answers
79 views

How to compare Smith–Waterman algorithm implementations?

Assume that you have two implementations of the Smith–Waterman algorithm (with what ever heuristic they apply to speed up) for local sequence alignment of genomic sequences. I would like to know if ...
2
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1answer
39 views

Scoring matrices in BLAST

I was reading wikipedia page on BLAST It says that scores are created by comparing the word in the list in step 2 with all the 3-letter words. By using the scoring matrix (substitution matrix) to ...
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1answer
45 views

Get Parent GO terms of GO term vector?

I have a vector of GOIDs that are specific GO IDs outputted from an enrichment analysis. I want to cluster my GOIDs by their parent GOID term. I used GOstats to do my enrichment analysis, and I have ...
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13 views

Quantifying the number of fragments from RAD library

I have a series of single-end reads from a RAD library of 48 uniquely tagged individuals in fastaq format. The data comes from a small MiSeq run. I want to know the number of unique fragments per ...
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1answer
81 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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2answers
28 views

What amount of genes co-expressed should be expected in a tissue?

I am working with gene expression microarrays of tumor tissues and I want to use a program to find the clusters of co-expressed genes in order to know if some particular genes are co-expressed with ...
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0answers
24 views

Query individuals with both WGS and RNA-Seq data

Using the SRAdb R package, I am looking to query individuals who possess both WGS and RNA-Seq data on the SRA. So far I believe I have been able to query specific samples with both WGS and RNA-Seq ...
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2answers
51 views

How to assess if biological measurements follow a normal or a log-normal distribution

I am using a dataset composed by $m$ samples and $n$ features (genes). Each data point is real number. I want to understand how to preprocess data before analysis, in particular: do data points ...
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2answers
20 views

BLAST with minimum E-value cutoff

It's easy to set the maximum E-value threshold in a BLAST request. I need to set the minimum E-value. Does anybody have any suggestions?
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1answer
47 views

Deletion of codons at the start of a sequence in preparation for heterogeneous expression. Why?

I am reading a patent where they isolate a gene from cDNA constructed from RNA extracted from plant matter. The subsequent step (in preparation for heterogeneous expression in E Coli.) puzzles me: ...
2
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1answer
63 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
24 views

Calling Alterations in Exome Data

What are the main technical differences between accurately calling somatic point mutations vs copy number variation (CNV) in exome data? Side note: would you need other -omic data to accurately infer ...
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1answer
58 views

what do I need to use for protein protein interaction network

I would like to know what i should use to be able to build a PPI network. I have seen different structure for different techniques. for example sometimes the input look like this , each protein with ...
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0answers
37 views

how to build a PPI network? [closed]

I would like to know how to visualise a cluster of several proteins lets say I have a list of proteins ...
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0answers
22 views

map list of proteins into an already built network

I have a built reliable network which can be downloaded from here http://www.filedropper.com/mynetwork This network is bulit using Cytoscape. Now I have a list of proteins IDs, for example ...
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0answers
28 views

Questions about Genetic algorithm paper of Gilman and Ross

I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link ...
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2answers
39 views

R/Bioconductor query for a gene?

I'm fairly new to bioinformatics, so please be gentle ;0 Is there a way to query a particular gene using a script in R/Bioconductor? I'm particularly interested in Gene Ontology terms. There are ...
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19 views

Is there a place or tool from which I can find or generate genome data for epistasis detection?

I am busy researching a school project for my honors in Electrical Engineering. The project is to create a deep neural network to detect epistasis. I have very little knowledge in the bioinformatics ...
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1answer
36 views

NCBI EUtils. Get Homolog infromation using Gene ID

How to retrieve homologs information in xml or json format from NCBI using gene ID? I tried one URL: ...
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0answers
18 views

Looking for dataset of proteotypic and non-proteotypic peptide

I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science. Any advice how to find proteotypic and non-proteotypic peptides....
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0answers
51 views

How do I run each individual record in a multi-fasta file against a database using PSI-Blast?

I'm new to standalone blast+ and the linux terminal. I set the bash-profile to load the PATH and BLASTDB for my blast already, but I don't know how to use psi-blast yet. How can I do the search ...
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1answer
78 views

What is the transcriptome in layman's term?

I am new to the bioinformatics field and am trying to understand a research paper that includes some terminology without definitions. The term transcriptome in particular is banded around in the ...
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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 ...
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1answer
41 views

Parameters of Variant calling analysis [closed]

What is the good or stringent parameter for variant calling. At present using the DP > 10 and Q > 30 for Variant calling. Is it ok.? Thanks
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0answers
14 views

RNA-seq: Controlling FDR in multiple contrasts [migrated]

I'm working on a RNA-seq analysis project and I have come across a statistics problem. I have 3 groups and I need to look for differential expression for each pairwise comparison. Do I control the ...
3
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2answers
79 views

How much genomic variation one usually find within a given bacterial species?

If I find the exact starting position (say 1152471) of the coding sequence of a given gene in the genome of a bacterium, is the genome of the bacterium in general stable enough so that I can expect to ...
4
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1answer
245 views

What do the letters 'p' and 'c' mean in mutation descriptions?

Example: NM_000525.3(KCNJ11):c. 67A>G ( p. Lys23Glu) AND Permanent neonatal diabetes mellitus Does "p" stand for "polymorphism"? What does the letter "c" stand for?
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1answer
62 views

Nomenclature for mutations at specific nucleotide positions

I'm sure this is a basic question, but I couldn't find an answer anywhere. Let's say I'm provided with the location of a nucleotide as location as FGFR3:c.1843-35A>T. What does "1843-35" mean?
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2answers
495 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" (from-"GENEID"...
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1answer
45 views

ExAC Browser: What does a “dubious variant annotation” actually mean? [closed]

I wonder how a "dubious" variant annotation is exactly defined in ExAC. I couldn't find any further information neither at the variant's page nor in the FAQs. Link to ExAC browser. Link to variant ...
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1answer
39 views

Deducing protein sequence length from gene DNA sequence length

Is there a standard way to deduce protein sequence length from gene DNA sequence length of the gene coding for it? Naively I had assumed that ...
2
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1answer
69 views

What is membrane-partitioning free energy? Can it be simulated?

Firstly, is there a strict definition of the "membrane-partitioning free energy"? It is banded around in membrane biology, but I have never seen it strictly defined. The only non-scholarly site that ...
3
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3answers
53 views

Needleman Algorithm for Optimal Alignment of two Amino Acid Sequences

I want to compute the optimal alignment of two amino acid sequences as per the following definition from a patent: "The percentage of identity between two peptidic or nucleotidic sequences is a ...
3
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2answers
74 views

Computing Percent Identity between DNA / Amino Acid Sequence

What are some tools where I can input a pair of DNA sequences (or alternatively a pair of Amino Acid Sequences) and compute a percent similarity identity metric between them? Is BLAST the right ...
2
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1answer
136 views

How to interpret this cuffcompare result? Sensitivity over 100?

I run a cuffcompare: cuffcompare -r transcripts.gtf TransStandard_1.0.gtf I got the following result: ...
0
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1answer
50 views

Examples of biological turing machines [closed]

Are there any examples of biological Turing machines? And what can they do?
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1answer
29 views

How are unnatural amino acids modelled using insilico tools?

When the structure of an unknown protein containing amino acids other than the 20 known natural amino acids is modelled which method is primarily used in bioinformatics to solve the structure? what is ...
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0answers
18 views

How to Determine Sufficient Time for Melanoma Survivor to Be Considered Low Risk?

Regarding melanoma, how do we determine the minimum amount of time that a patient is disease free for them to be considered low risk? We are attempting to do survival analysis on RNASeq data from ...
6
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4answers
415 views

Compressing structural information in PDB files

There seems to be a lot of redundancy in PDB files. These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are ...
2
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0answers
84 views

What is the another use of de Bruijn graphs in bioinformatics except DNA assembly? [closed]

I implemented own generic de Bruijn graph, which I use for DNA assembly (alphabet: A, C, G, T). I try to find purpose of de Bruijn graph for another bioinformatics problems, if some exists. I want use/...
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1answer
66 views

Can exhaustive algorithms produce MSAs that are suitable for 3D structure modelling?

While predicting 3D structure of a protein through homology modelling, 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
50 views

Variant VCF: AD vs DP?

In my VCF file from GATK, I have the following definitions for AD and DP. ...
3
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1answer
96 views

Dnase data for GRCh38

This question below turned to be completely faulty. I don't have to do anything with DNase data for GRCh38. I asked it because of the file count difference between hg38 and hg37, which I thought to be ...