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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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 <...
1
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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 ...
13
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2answers
207 views

Can two protein secondary structures “overlap” in the PDB?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: ...
6
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3answers
123 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 ...
2
votes
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 ...
0
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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 ...
1
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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......
1
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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
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 ...
0
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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 ...
1
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2answers
79 views

How to predict the effect of a non coding SNP variant on the expressed protein?

I am writing a paper for non coding SNPs on patients with metastatic breast cancer. Having used a specific gene panel (NGS) of approximately 60 genes, I'm currently running out of ideas on what to ...
1
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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
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
vote
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 ...
2
votes
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 ...
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 ...
0
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0answers
30 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
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2answers
66 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 ...
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, ...
3
votes
1answer
47 views

Finding confidence level of miRNA disease associations

I'm an undergraduate computer engineering student, and I have a project about bioinformatics. In this manner, I need to find prediction( or association I'm not sure the correct terminology) confidence ...
4
votes
1answer
191 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
12
votes
2answers
215 views

How can we verify predictions of protein folding in silico?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
0
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0answers
32 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 ...
3
votes
4answers
152 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 ...
1
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1answer
32 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 ...
1
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0answers
65 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 ...
4
votes
3answers
268 views

What is the state-of-the-art algorithm for multiple sequence alignment?

Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment? How big is the need for better algorithms? How many sequences need to be alignment in a ...
0
votes
1answer
57 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 ...
4
votes
1answer
219 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 ...
6
votes
1answer
122 views

How can I make a protein interaction/protein-complex network?

Let's say I have a list of proteins ID. I would like to know whether I can find any complex based on that list. Any example, explanation is appreciated. An example input is what you see below. What ...
1
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0answers
40 views

How do I retrieve electronic annotation from Uniprot and GO records that relates to molecular function?

I'm interested in the endonuclease activity of the G3BP1 gene, specifically the uniprot record Q13283. An external link guides me to UniprotKB-KW electronic annotation. How can I retrieve valuable ...
0
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0answers
46 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
50 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: ...
21
votes
2answers
25k views

What is the difference between local and global sequence alignments?

There are a bunch of different alignment tools out there, and I don't want to get bogged down in the maths behind them as this not only between softwares, but varies from software version to version. ...
6
votes
1answer
262 views

Sequence evolution simulation tool

I'm looking for a tool to simulate sequence evolution given a specific mutation model and birth-death model. I'm aware of tools and packages like INDELible, Seq-Gen and PhyloSim, but they simulate ...
4
votes
1answer
169 views

How do I make a multiple sequence alignment (MSA)?

I have a DNA sequence that makes protein 1, but now I have asked to: compare the amino acid sequence of protein 1 with nine homologous proteins and make a multialignment of the sequences. Determine ...
5
votes
1answer
56 views

Data on Gene Position in Human Genome

I am trying to get some data on gene position in the human genome and I need some help What I tried I downloaded ...
2
votes
1answer
52 views

How many paraphyletic groups can be formed from a phylogeny?

How many paraphyletic groups can theoretically be created from this phylogeny? I found (2n)-2. Is this correct? This is not homework nor exam, just a question about paraphyletic groups.
4
votes
1answer
57 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 ...
1
vote
1answer
24 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 ...
2
votes
3answers
78 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 ...
1
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0answers
38 views

How to construct tumor phylogenetic tree?

I would like to know if anyone has tried any software that constructs tumor evolution trees where the trunks represent the common mutations and the private alterations are noted on each branch. I can ...
1
vote
1answer
48 views

Data on Recombination rate and Gene Positions in Humans

I am looking for estimates of per base pair recombination rate in humans and indication on gene positions. The goal is to be a able to plot recombination rate in the y-axis and position (in bp) along ...
0
votes
0answers
40 views

Extracting the donor/acceptor sites from mRNA sequence(PERL/ DNA transcription)?

I have the following program that I am analyzing and trying to understand. Overall purpose of it is to put out, based on the option selected, the set of introns, exons, acceptor sites , or donor sites ...
2
votes
1answer
55 views

Protein-protein interactions search

I used STRING db in order to find all the interactions of the precursor protein APP. What I specifically need is a confirmation (supported by some article and experiments in it). But significant ...
5
votes
1answer
98 views

Why do we encode information in DNA in binary and not in base 4?

I recently read an article about Harvard scientists encoding 700Tb of data in DNA strands. But they encoded the information in base 2, so T and G was a 1 and C and A was a 0. But why binary? Why didn'...
6
votes
1answer
104 views

Software recommendation for protein in electric field modeling? [closed]

I'd appreciate a suggestion for software to compare models of two proteins in an alternating electric field. The more detail, or perhaps direction towards an existing and similar paper, the better. ...