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)

5
votes
1answer
95 views

Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
0
votes
1answer
77 views

Does increasing the value of k in k-fold coverage requires more memory?

Study: Here is what is k-fold coverage which is know as sequence coverage. According to this, 2-fold coverage means the whole DNA is sequenced more twice in average. Question: If I have a genome ...
1
vote
0answers
24 views

Degenerate primer designing software

Can any one provide online free degenerate primer designing software. I have tried couple of them like CODEHOP is one where BLOCK formatting step finding difficulty, can anyone help me out....
1
vote
1answer
61 views

Do the BLAST scores have any relation between them?

Is there any relation among the BLAST scores (E-value, similarity, identity, gap, bit score)? Is the e-value score for an alignment proportional to other scores, such as similarity score (i.e. the ...
2
votes
1answer
71 views

Is there a free software for manual sequence annotation?

I'm looking for a software that would allow me to make a quick graphical annotation of the structural features of a sequence. Something that would look like what you get in jalview, with your sequence ...
0
votes
1answer
34 views

Why does uniprot sometimes not label single-pass transmembrane proteins as “anchors”?

Currently, section 3a) of unitprot TRANSMEM reference page divides single-pass transmembrane proteins into 4 types: ...
5
votes
1answer
84 views

How many genes does D. melanogaster have?

Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, ...
0
votes
1answer
60 views

results of FgenesH and GenScan

Why FgenesH and Genscan don't give good results as I have prdicted number of genes of Chromosome 16 which according to NCBI are 86 but the results I have obtained are 57 genes predicted by FgenesH and ...
0
votes
0answers
33 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?
2
votes
1answer
42 views

How to find conserved residues across species?

I want to identify if certain phosphorylation sites are conserved for protein X across humans and yeast. I know from MS data that there are 4 phosphorylation sites in Human protein X. In order to ...
2
votes
2answers
105 views

How to build a trimeric protein structure from monomeric PDB file?

Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full ...
-1
votes
1answer
57 views

Difference between various evolutionary terms [closed]

Could someone kindly explain me the difference between Phylogeny, Phylogenetic Tree, Evolutionary Trees, Phylotype, Clusters, OTU (Open Taxonomic Units). Or if possible please do suggest me a ...
1
vote
1answer
37 views

gene transformation from plant to plant - transgenic plant

I want to know if the expression of a transfered gene depends on source of the gene, if e.g.: 1] I isolate a gene from plant and transfered it to the same plant? 2] I isolate a gene that is highly ...
1
vote
1answer
61 views

How is the probability of a sequence occuring with BLAST calculated?

What is the probability that a given nucleotide/amino acid sequence will occur in the whole database program BLAST searches in? How this probability is calculated?
3
votes
1answer
29 views

Gemini usage of --sample-filter

I am using gemini to query databases made from vcf files, which contain data from multiple samples. However, I need to query data only from one sample, (for which I currently use grep to filter the ...
1
vote
0answers
32 views

Biological modeling languages - some basic issues

I am trying to get used to with couple of modeling languages in biological context like SBML, BioPAX, Kappa and BEL. Some basic issues came up to my mind that are unclear to me even after a lot of ...
1
vote
3answers
43 views

importance of cDNA sequencing of a specific gene in different plants

i want to know what if i made a sequence of cDNA of a specific gene in different plants - what is the important from the sequence and can if found difference between plants , and can i use this ...
1
vote
1answer
63 views

From STRUCTURE to FSTAT format

From numerical simulations I output a file that is input to STRUCTURE (Hubisz et al. 2009). I now realize that I would need to process my data with FSTAT (Goudet 1995). Both are text files. Is there ...
2
votes
2answers
169 views

In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?

I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis. I also understand cloning can be a ...
2
votes
1answer
48 views

In DNA sequencing, is “mate pairs” synonymous with “paired ends”? If not, how do they differ?

By just looking at Roach et al's paper I get the impression that they are the same thing, and the Wikipedia URL for the former is a redirect to the latter. However, I suspect they are not exactly the ...
3
votes
1answer
190 views

How to perform a DNA structural alignment in pymol

How can I "fit" two DNA structures having different nucleotide sequences in pymol? I would like to use the structure of a DNA binding protein in pdb (1h9t), which is bound to DNA in the pdb file, ...
2
votes
2answers
68 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 ...
2
votes
2answers
48 views

How does one find the corresponding SNPs in the pair of chromonosmes in a FASTA file?

You might say I'm an amateur bioinformatician, or trying to become one. I have a BAM file, from which I have succeeded, using UGENE , in extracting consensus data in FASTA format. I now see a single ...
1
vote
1answer
34 views

Metrics or operations on genome sequences in human genomic research?

Edit distance may be an important metric for measuring the similarity of two genome sequences. For example, if A = GCAATT and B= CGAATA, then the edit distance of A and B is 3. Such a metric is ...
1
vote
1answer
50 views

How to Determine the Most Conserved Sequence from BLAST Result?

I used BLAST to find the best aligned DNA sequence to my query sequence. The BLAST result shows a number of sequences that it calculated to be the best aligned sequences to the query sequence that I ...
0
votes
0answers
30 views

How to find gene variation in NCBI?

I am looking for variations of my gene so that I can design a primer. But, I do not know how to found the relative links in NCBI. Where can I start?
9
votes
1answer
118 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 ...
1
vote
1answer
45 views

What does uniprot consider “unambiguous” evidence for the subcellular domain of a protein?

Uniprot has annotation for subcellular location of protein domains. This topological domain information of proteins is under the TOPO_DOM flag. In most cases the ...
1
vote
1answer
61 views

How to annotate a .broadpeak file with 9 columns?

I have this peak file I retrieved from an ENCODE chip-seq matrix. Its .broadpeak file looks like this: ...
1
vote
0answers
45 views

Running (standalone) PSI-BLAST Against Multiple Queries

I'm new in standalone blast+ and in 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 ...
0
votes
1answer
64 views

Does a DNA sequence has its own derivation tree or pattern?

I am new to bioinformatics and natural language processing. In linguistics, they have Treebank - derivation/parse tree for each sentence. For example, a sentence "Sara sleeps" can be visualized by a ...
2
votes
1answer
46 views

Conserved acetylation sites in a given protein

I want to identify potential conserved Acetylation sites in protein X. As it is known, acetylation happens in Lysines (K), thereby I would like to identify conserved K residues for protein X during ...
2
votes
1answer
174 views

How does one calculate the amount of oxygen produced by trees?

I'm currently working on a project to measure the impact of tree planting. Calculating the amount of oxygen seems harder than I imagined. Of-course there's the type and size of the tree and the ...
1
vote
2answers
60 views

yeast protein secondary structure

i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous ...
4
votes
1answer
158 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 ...
0
votes
2answers
39 views

Data Retrival from the GenBank?

When I go to NCBI & Select nucleotide option there and in search box write For Example CNGA3 gene the page shows that there are 553 items.I know the method of downloading or retrieving the One ...
1
vote
0answers
60 views

How do you create a .snp datafile?

I'm looking to use the software DIYABC 2.1.0 to apply approximate bayesian computing (ABC) to some resequenced data that I have. The resequenced data is in FASTA format however, and the software ...
1
vote
0answers
27 views

Batch several sequences for absent restriction sites

I have a collection of about 120 7kB sequences I would like to check for ether a list of specific restriction sites, or what restriction sites might be absent in all of them. Is there a app or ...
3
votes
1answer
57 views

How to predict a mRNA secondary structure with a large sequence?

When I use some web servers to predict a mRNA secondary structure, I find they always required in a small size sequence. If I use a long sequence and cut it into small parts, do these small parts ...
2
votes
1answer
35 views

Why my base-quality in alignment is not perfect?

I have a fasta file with some DNA sequences. I would like to simulate next-generation sequencing reads from it. I'm doing it without any base error and mutation error. ...
0
votes
0answers
39 views

Shortest path and influenza spread

I have been researching on the applications of the shortest path problem to biology. I thought about modelling the spread of influenza virus and wondering if there was previous research on the topic. ...
0
votes
0answers
25 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: ...
1
vote
1answer
13 views

num_tol_term in PeptideProphet result

What is the meaning of the num_tol_term attribute in a PeptideProphet (pep.xml) search_hit? ...
3
votes
2answers
142 views

Is there a database of cell images?

We're working on an algorithm for processing images of cells, similar to but much more basic than Cell Profiler, and we are looking for a large database of cell images to test our software. Can anyone ...
2
votes
1answer
81 views

What is biological intuition?

Whenever I read or learn about prediction tools or aligners or motif detectors, I also hear that they are lacking in something called biological intuition. But I haven't been able to find a solid ...
2
votes
0answers
41 views

What program was used to create this visualization of a neighbor-joining tree?

I know there are many programs out there to visualize neighbor-joining trees in phylogenetics. I have a tree in Newick format. Does anyone recognize the features of this image as coming from a ...
1
vote
0answers
73 views

How to identify a pseudogene to a specific protein coding genes?

Pseudogenes are those sequences in the genome that bear similarity to specific protein coding genes, but nevertheless are unable to produce functional proteins due to existence of frameshifts, prema- ...
4
votes
2answers
134 views

Do the bacterial species X, Y, Z code for proteins A, B, C?

My PI has assigned me a task to gather evidence to determine whether or not a list of particular species of Campylobacter and Helicobacter code for a list of several proteins. To put it simply I’ve ...
1
vote
1answer
104 views

How to find a Cancer PPI network data [closed]

I need a Protein Protein Interactions network of Cancer (any type - just I want a PPI of any type cancer), I search and see DIP PPI and .... How to specify that is Cancer PPI and how to get a PPI of ...
1
vote
1answer
70 views

How to interpret the simple sequence repeat (SSR) on the coding sequence, but not the related protein sequence?

I have predicted some SSR repeat on the gene of interest using SSRLocator program, which the result creates a question for me. Please consider the below sequence, which is part of gene sequence of ...