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14 votes

If we sequenced the genome of every species, would all phylogenies agree?

Horizontal gene transfer Don't expect to have a tree! Horizontal gene transfer happens and therefore we would end up with a network, not a tree. Gene trees Different DNA sequences have different ...
Remi.b's user avatar
  • 68.1k
13 votes

How are DNA virus cladograms actually calculated in practice? Is the procedure different for RNA viruses? Are these processes somewhat subjective?

How are DNA virus cladograms actually calculated in practice? A cladogram, or phylogenetic tree1, is constructed by comparing similarities and differences between organisms, and placing those within ...
Darlingtonia's user avatar
  • 2,582
11 votes

Is it possible to establish a newer animal model completely based on Bioinformatics studies?

It is naïve to think that the extent of protein similarity is sufficient to determine what is the best animal model for a human disease. The physiology of the animal and the question of compensatory ...
David's user avatar
  • 25.7k
9 votes

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

Lowercase letters indicate repeat-masked regions. N's represent gaps. See: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/S4Sx8UdJAwM/tLTpVVzdhFMJ
Ann L's user avatar
  • 91
7 votes

How are DNA virus cladograms actually calculated in practice? Is the procedure different for RNA viruses? Are these processes somewhat subjective?

Disclaimer: I'm not a bioinformatician, though I occasionally dabble in it, so I may well have some things incorrect. Please feel free to correct or make your own answer. As I see it, you are asking ...
bob1's user avatar
  • 12.1k
6 votes
Accepted

What is the biological significance of k-mer counting?

The applications for counting the k-mer occurences in a sequence are: building de Bruijn graphs [1] for de novo assembly from very large number of short reads, produced by next generation sequencing, ...
Gergana Vandova's user avatar
5 votes
Accepted

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

The FTP download files are documented on the UCSC site (from which they also may be downloaded from a web browser). The page for the human genome is http://hgdownload.soe.ucsc.edu/goldenPath/hg38/...
David's user avatar
  • 25.7k
5 votes
Accepted

What is the significance of cysteine in a protein sequence?

What can I infer if I get a high percentage of C from a protein sequence? A highly stable structure that is likely found in the extra-cellular space. Cysteine can form a disulphide bond with ...
James's user avatar
  • 11.3k
5 votes

Comparative evolutionary study: is amino acid or nucleotide comparison more useful?

Each has its own utility, depending on the time-frame you are looking at. For evolutionary studies, you need variation, but not so much variation that one substitution at the same position overwrites ...
Karl Kjer's user avatar
  • 7,663
5 votes

Comparative evolutionary study: is amino acid or nucleotide comparison more useful?

The Answer It is correct that the product of the conceptual translation of a nucleotide sequence into an amino acid sequence results in the loss of certain information present in the former. An ...
David's user avatar
  • 25.7k
5 votes
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Meaning of ‘motif’ in molecular biology

Meaning of Motif in Molecular Biology In English the word, motif (borrowed from the French), has a variety of meanings in different areas. The one that is borrowed in molecular biology is that of ...
David's user avatar
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5 votes
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What is the difference between 4th generation sequencing and NGS?

I think that all of this is pure marketing and can be safely ignored. There is no basis for the generations of sequencing in chemistry or instrumentation, except possibly that second-generation (...
Maximilian Press's user avatar
5 votes
Accepted

What results would come from DNA analysis of several different types of DNA mixed together?

You may be interested in commercially available meat testing kits - DNA kits have been widely used to detect what certain food products are actually (or are actually not) made of. Some kits are ...
Nuclear Hoagie's user avatar
4 votes
Accepted

What are "+" and "Ar" in consensus binding sequence of amino acids?

Ar means aromatic and + means positively charged residues. However, this is not a standard code (as of now). From the same ...
WYSIWYG's user avatar
  • 35.6k
4 votes

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

Sequence in caps are usually regions of interest, such as exons. N in the DNA alphabet refers to "unknown nucleotide" It can refer to any of A/T/C/G when the actual underlying base is unknown.
Ram RS's user avatar
  • 276
4 votes
Accepted

What do Illumina HiSeq/MiSeq paired end reads look like?

Where the reads found in R2 are the reverse complement of those found in R1. This statement seems incorrect. Paired-end reads comes from opposite ends of a fragment (you could learn the reason it ...
Maxim Kuleshov's user avatar
4 votes

How to check if a fastq file has single or paired end reads

This is complementary answer to what @gc5 provided. For cases that are using "the second notation" which looks like: ...
Mehrad Mahmoudian's user avatar
4 votes
Accepted

List of proteins by number of amino acids / chain length

You can find the data you need in the Protein Data Bank. Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, ...
marcin's user avatar
  • 449
4 votes
Accepted

Methods for microbial identification in soil

16S and ITS techniques try to identify organisms in your samples by amplifying short, 'barcode' sequences from each organism's DNA, and using those short sequences to try to identify the organism they ...
Jay Moore's user avatar
  • 827
4 votes

What do lower case nucleotides mean in this gene sequence?

The case refers to the degree of conservation of a particular nucleotide in the consensus sequence. Highly conserved nucleotides are written in uppercase. At positions where the sequence varies, the ...
canadianer's user avatar
  • 17.7k
4 votes

Lysozyme amino acid sequence: N-terminal extension

If you scroll down through the uniprot entry you will come to a section with the heading PTM/Processing. From this you can see that the first 18 amino acids are a signal peptide. You can learn more ...
tyersome's user avatar
  • 5,598
4 votes
Accepted

Why are some protein sequences known but their 3D structure isn't?

Protein sequencing is a nicely constrained problem: you have a one-dimensional sequence of amino acid members, which come from a limited set of options (made a bit more complicated by post-...
Bryan Krause's user avatar
  • 45.7k
4 votes
Accepted

Sequence of DNA

DNA sequence is what we call a string of nucleotides in the DNA polymer, such as GATTACA, representing a chemical structure wherein each letter ("G", &...
Maximilian Press's user avatar
4 votes
Accepted

Why UniRef representative sequences in UniProt are so long?

This is a good question, but there are a few things going on. There is a subtlety about what you're asking: do you want to know the average length of a protein sampled from a cell, or the average ...
ksdjnf's user avatar
  • 186
3 votes

Standard practice for generating rarefaction curves from Next Generation Sequencing data

I actually work in the same group as Chris (QIIME author), so I hope this helps: An explanation he gave to us a while back about the basis of rarefaction curves is just to give an indication of ...
Joe Healey's user avatar
  • 1,301
3 votes

Fold Coverage of sequence read?

Fold coverage is often derived with respect to a genomic locus, not a read. In sequencing experiments, fold coverage of a genomic loci (coordinate along a reference assembly) will be the number of ...
Noushin's user avatar
  • 176
3 votes

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

The IUPAC Nomenclature symbol table for RNA and DNA nucleotide sequences (via Wikipedia)
mdperry's user avatar
  • 3,517
3 votes
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Distribution of Exon and Intron Sizes

At the command line: ...
Devon Ryan's user avatar
3 votes
Accepted

Which DNA sequence will have higher melting temperature: CCCCCC... or GCGCGC...?

The dependence of melting temperature on different dinucleotide pairs was experimentally measured; the meting temperature calculator is based on those results. Based on these results, you would see ...
WYSIWYG's user avatar
  • 35.6k
3 votes

List of proteins by number of amino acids / chain length

In the UniProt Knowledgebase, you can have your proteins sorted by protein length, e.g. in this query for all human proteins with a cross-reference to PDB: https://www.uniprot.org/uniprot/?query=...
Elisabeth.Gasteiger's user avatar

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