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
vote
1answer
36 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
60 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
28 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
40 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
55 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
144 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
170 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
1answer
51 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
45 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
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 ...
0
votes
1answer
42 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
57 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
43 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
45 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
145 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
59 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
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 ...
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
52 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
26 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
38 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
24 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
136 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
77 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
39 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
67 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
133 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
82 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
66 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 ...
2
votes
3answers
460 views

What is the biological significance of finding palindromes in DNA sequence?

I found a function called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of ...
3
votes
1answer
51 views

blastn: What substitution matrix is used?

I'm currently working aligning sequences, and I need to compute similarity between pairs of DNA 'words' of a particular length. For amino acids I am able to use the substitution matrices in Biopython ...
1
vote
2answers
57 views

How can I find some pieces of the genome of a microorganism?

I have figured out how to download the fasta of the genomes of microorganisms, for example the botulism bacteria and the spirulina algae. However, I want to find a fasta file for some significant ...
0
votes
1answer
128 views

Normalised gene counts to edgeR/DESeq2?

Both very popular differential expression packages assume a raw gene matrix count. This makes sense because the statistical model models the library depth. But what if I normalize my counts with say, ...
0
votes
1answer
55 views

Expected dS/dN ratio for exome

I am trying to determine whether or not my sequencing data has more/less non-synonymous mutations than would be expected. My understanding is that there is some fixed ds/dn ratio for the human exome ...
1
vote
1answer
58 views

Is studying complete mitochondrial genome need biological lab work?

The research complete mitochondrial genome study done on species: Juema pig Sus scrofa (Suina: Suidae) from southern Gansu red rainbowfish speckled dace, Rhinichthys osculus white char Salvelinus ...
0
votes
4answers
217 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 - ...
3
votes
1answer
131 views

What is the last heavy atom of an amino acid?

I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it ...
0
votes
1answer
91 views

difference in genetic instuctions between male and female [duplicate]

I'm a computer science graduate so please bear with me the following computer program : mov ecx, -1 INC ecx consist of 2 instructions (mov,inc) each working on specific data , can genetics ...
1
vote
0answers
84 views

How to interpret this cuffcompare result? Sensitivity over 100?

I run a cuffcompare: cuffcompare -r transcripts.gtf TransStandard_1.0.gtf I got the following result: ...
2
votes
2answers
89 views

It's right to say coding sequence is part of exon sequence?

Some basic ambiguities making me confused. I downloaded 5'UTR, CDS, 3'UTR, and exon sequences, separately from Biomart for a gene P4HA2 (Homo sapiens) and found some simple sequence repeat (SSR) on ...
2
votes
1answer
53 views

Why the length of UTR in the genomic sequence of gene X is too much longer than the same region in the corresponding Refseq mRNA sequences?

I'm browsing in the UCSC genome browser and found that the UTRs length of KIAA0040 gene in the genomic sequences is too much longer than the corresponding the Refseq mRNA sequence. In fact, the total ...