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 ...

learn more… | top users | synonyms (1)

-1
votes
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 ...
2
votes
1answer
202 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?
0
votes
1answer
29 views

Parameters of Variant calling analysis

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
1
vote
1answer
48 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 ...
0
votes
1answer
33 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 ...
-1
votes
0answers
12 views

Is there a way to convert/export track files (.trc file) generated from Media Cybernetics Image Pro Plus to .mat file type? [on hold]

I am trying to export these files so that they can be used with a matlab based automated behavior classification software JAABA. At the very least I would like to figure out a way to read the format ...
0
votes
0answers
33 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: ...
0
votes
1answer
38 views

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

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 ...
3
votes
3answers
49 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
votes
1answer
28 views

“Other” peptides in 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" ...
3
votes
2answers
65 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 ...
0
votes
1answer
49 views

Examples of biological turing machines [closed]

Are there any examples of biological Turing machines? And what can they do?
-1
votes
1answer
23 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 ...
0
votes
0answers
17 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 ...
0
votes
0answers
19 views

Skip estimateDispersions() DESeq2 [closed]

In my experimental design, I have 20 libraries, coming from 20 F2 interspecific hybrids, meaning every genotype is different. 10 individuals are tolerant and the other 10 are sensitive to a specific ...
1
vote
1answer
66 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 definitions which I looked up on the internet, but couldn't find the proper definition of following:...
2
votes
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/...
1
vote
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
votes
1answer
94 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 ...
1
vote
1answer
33 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
votes
0answers
28 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
votes
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 <...
1
vote
1answer
50 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......
0
votes
1answer
41 views

Variant VCF: AD vs DP?

In my VCF file from GATK, I have the following definitions for AD and DP. ...
0
votes
1answer
63 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 ...
1
vote
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?
1
vote
0answers
30 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 ...
0
votes
2answers
47 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 ...
1
vote
1answer
54 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, ...
1
vote
0answers
23 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
vote
0answers
35 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
vote
1answer
57 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
votes
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
48 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
votes
2answers
61 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
votes
1answer
75 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 ...
1
vote
2answers
64 views

What makes DNA sequences most different/recognizable from a biological perspective? [duplicate]

We can pretty easily quantify the amount difference between two different strings/sequences of characters. For example, if we take the words trebuchet and trebucket, we can say they have a Levenshtein ...
0
votes
0answers
29 views

How to search for all human diseases associated with a inversion on chromosome 22?

Is there any way to search for all diseases that associated with inversions on chr22? I found some online research databases like OMIM and disgenet but I don't know the correct nomenclature on how to ...
1
vote
1answer
27 views

Taxonomic clasification of BLAST output

I am working with Next Generation Sequencing. I BLASTed the bovine de novo assembled contigs to the NCBI nucleotide database. I got a matching with a lot of species i.e. different kind of bacteria, ...
0
votes
0answers
29 views

Where to go next with clustered C elegans neuronal time series

I'm doing some independent research with the C Elegans nervous system (with the OpenWorm project) and was looking for some guidance as to where I should go next. Right now, I'm dealing with calcium ...
4
votes
1answer
217 views

How the genome assembly be done after k-mer counting?

As far I know, before assembly of a genome, all k-mers from read should be counted. But after that, how the genome assembly be done? Is there any other thing needed along with k-mer counts? How ...
1
vote
0answers
63 views

Reading BLOCKS database into Python or R [closed]

Are there any methods in programming languages that have been developed for reading the BLOCKS database? http://blocks.fhcrc.org/ What I want to do is read in the database file and compare sequences ...
3
votes
4answers
123 views

Significance of upper-case, lower-case and Ns in UCSC DNA files

I have downloaded human chromosome's data from UCSC FTP. Some part is in small alphabets and some is in large alphabets. Does it show the coding and non-coding region? Here is an example from the ...
0
votes
1answer
56 views

Online multiple sequence alignment with constraints

This is probably a naive question. I have accesssed the Clustal Omega online multiple sequence alignment tool at http://www.ebi.ac.uk/Tools/msa/clustalo/ for the first time, but I think I need to ...
1
vote
1answer
31 views

Difference between pulse coupling and diffusive coupling In biological oscillators

What are the differences between pulse coupling found among neuron cells and diffusive coupling found in cells that exhibit calcium waves? Moreover, in both methods, is it a strict requirement that ...
0
votes
0answers
45 views

How to view selected chromatin states (i.e enhancers) on the UCSC browser?

I'd like to overlay enhancer regions with SNPs in a particular locus using FunciSNP. I can view all the chromatin-state annotation from chromHMM ( Roadmap Epigenomics Integrative Analysis Hub) in the ...
4
votes
1answer
49 views

How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?

I have a list of taxids that looks like this: 1204725 2162 1300163 420247 I am looking to get a file with taxonomic ids in order from the taxids above: ...
0
votes
1answer
22 views

Measuring tumor heterogeneity [closed]

I would like to ask if there's any method (established or not) in order to quantify heterogeneity found in mutations occuring in primary neoplasms and metastatic lesions (either common or private) and ...
4
votes
1answer
56 views

How can I obtain a computer readable model of Dr. Gerhard Michal's biological pathways map?

I want to run simulations of various metabolic pathways – the project could end up becoming quite large, and having a machine readable chart would make thing a lot easier. Does anyone know if there is ...
0
votes
1answer
37 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 ...