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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Question: 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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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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24 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
38 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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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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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
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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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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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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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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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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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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18 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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2answers
38 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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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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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 ...
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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
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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2answers
85 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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1answer
38 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 ...
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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: ...
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1answer
44 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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3answers
52 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 ...
2
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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
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 ...
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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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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 ...
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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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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
53 views

Output of clustalo on (1.2.1) on ubuntu 14.04

I am trying to align the following 8 sequences using clustalo on ubuntu terminal using the following command. But I am not getting the right output. ...
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 ...
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1answer
38 views

Distribution of Exon and Intron Sizes

Goal I am trying to get a distribution of Exons and intron sizes in Three-Spined Stickleback (Gasterosteus aculeatus). Data downloaded I downloaded some data from Ensembl. More precisely, I went ...
3
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0answers
29 views

filtering a BLAST search to only include a certain protein sequence

I am performing a BLAST search and I need to filter the output to a certain family of proteins. Specifically, I need to get matches within the CYP152 family of the Cytochrome P450 proteins. I can ...
2
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1answer
104 views

How to retrieve logical expression (KO based) for reactions from KEGG?

Whether a module is complete or not can easily be checked by evaluating the Definition entry associated with the module; e.g. in module M00010, it is given by <...
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1answer
57 views

Coordinates of amino acids in a protein sequence [closed]

In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids MKL......
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1answer
49 views

Variant VCF: AD vs DP?

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

What are Codominant vs Dominant Genetic Markers?

When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions. Foll and ...
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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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0answers
32 views

My BRIG run is suspiciously quick. What is a typical length of time for a run?

I use the BRIG (BLAST Ring Image Generator) program to compare prokaryote genomes. It executes a local BLAST+ and visualizes the results as rings around the reference genome. I downloaded three ...
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2answers
56 views

Simple computational biology project for AP Biology class. Ideas? [closed]

Our teacher assigned us a project to do with an extremely open-ended prompt and it should be completed within a month. I was planning on doing something related to computation and evolution in terms ...
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1answer
61 views

where can I find a full list of examples of data types in biology? [closed]

I have no background in biology and I would like to build a collection of the data types in biology. I start searching and reading bout that and found there are 7 data types: 1-Sequences: DNA, RNA, ...
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0answers
24 views

Loooking for dataset of proteotypic and non-proteotypic peptide

I'm experimenting with peptide prediction using machine learning. I need some data for testing. I already have one dataset, but I need another one or two for verification. I'm looking for data for a ...
1
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0answers
36 views

Similarity with protein sequence [closed]

I have chosen a protein sequence and I want to record the sequences having similarity more than 85% of the chosen sequence. How can I find it using FASTA?
1
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1answer
86 views

How to interpret Percent identity matrix created by Clustal Omega?

I did a multiple sequence alignment using Clustal omega. checked similarity for 3 protein sequences : aspartyl aminopeptidase [Homo sapiens], aminopeptidase P (APP) [Plasmodium falciparum 3D7], yeast ...
2
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0answers
36 views

Estimated protein size using CDs data [closed]

The number of amino acids in a protein is important to predict their size. I used coding DNA sequence (CDs) to predict the average of the protein size of E.coli k12 from a sample provided by the ...
2
votes
1answer
49 views

miRNA_ID to GENE_SYMBOL conversion

I have a list of miRNA IDs and a list of mRNA IDs and they are from Mus musculus species. I have converted the list of mRNA IDs to gene symbols by a list of data that was exist in NCBI and miRNA IDs ...
3
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2answers
69 views

What is the most appropriate way to normalize gene expression data?

This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for ...
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 ...