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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22 views

Programs/software to graph biological data

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 ...
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1answer
53 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 ...
17
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1answer
732 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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0answers
22 views

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

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 ...
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12 views

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

I know that a deceased relative had a genetic test made that showed a result of a Chromosomal inversion on chr22 but I don't know what type and where is the inversion until I get the full medical ...
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1answer
21 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, ...
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0answers
37 views

Is there a package or a software to calculate an holey fitness landscape?

The holey landscape is interesting to enable the population to move from an adaptive peak to another without crossing a valley of low fitness. A fitness landscape is computable in R with a GAM model ...
3
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1answer
46 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
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1answer
183 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 ...
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0answers
37 views

Is there a separation between hard- and software in the brain? [closed]

In a computer, you have (very simplified) the software, imprinted on hardware. Comparable to the cylinder in a music box that encodes the music. But when I sing a song I can´t imagine that software ...
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2answers
186 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 ...
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19 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 ...
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1answer
23 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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0answers
10 views

Organization braincells [closed]

Why do microchips have a flat architecture, in contrast to neurons, and why is the energy supply of chips not divided over all the parts of the microchips, as it is in neurons?
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4answers
78 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 ...
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1answer
25 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 ...
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0answers
59 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
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3answers
253 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
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1answer
51 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 ...
3
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1answer
209 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 ...
5
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1answer
98 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 ...
0
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1answer
67 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
54 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 ...
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0answers
36 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 ...
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0answers
34 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 ...
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0answers
50 views

Disease-Associations For Protein Analysis? [closed]

I would like to get access to any protein database of disease-associations which I could use home with biomechanical signals in different systems. A similar software to what I am looking for is the ...
4
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1answer
40 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: ...
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2answers
21k 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
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1answer
234 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
151 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
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1answer
50 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
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1answer
50 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
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1answer
55 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
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1answer
20 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
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3answers
70 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 ...
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0answers
28 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
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1answer
41 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
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0answers
31 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
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1answer
52 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
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1answer
82 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 ...
6
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1answer
100 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. ...
4
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0answers
35 views

How many residues can a reliable ab initio structural model contain?

A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be ...
9
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1answer
113 views

How can I find the mRNA sequence for a specific prokaryotic gene?

What I want to find out is the start of the transcription for a specific gene, how long the UTR is before the actual coding sequence starts. I've looked at various databases like NCBI Gene, Refseq or ...
3
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1answer
60 views

Understanding common identifier codes (IDs) in biology databases

I know this is very basic but I would like to understand it and it's difficult to know where to begin with a new database. I have the output: ...
4
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2answers
54 views

Grouping OMIM disease codes

I have ~100 sets of genes, and each set includes between 2 and 70 genes. I'd like to perform an enrichment analysis on each of these sets to test if they're enriched for OMIM disease labels. However, ...
2
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1answer
335 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 ...
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0answers
15 views

What is the best test for SNV clustering?

I am looking for a method to cluster single nucleotide polymorphisms based on clinicopathologic data (mainly receptor immunoistochemistry). So far, I've came up with only two that handle dummy ...
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2answers
53 views

how to compare Smith–Waterman algorithm implementations?

Assume that you have two softwares of 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 for sure ...
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0answers
24 views

Gene expression data [closed]

I am using gene expression data for the classification of cancer. I need to know how the values are processed. within what range the values will be? What does the negative value means? How can I do my ...
0
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4answers
218 views

How to convert FASTQ file format into GTF file format?

I have a plenty of FASTQ files (FASTQ is a standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer) and need to convert them to GTF format (gtf - ...