Skip to main content
7 votes

Can two proteins sharing a few domains be considered homologous?

Homology means shared evolutionary ancestry. Sequence similarity is often used as a proxy for homology but inferences should be made with care. The similarity between two genes/proteins should not ...
WYSIWYG's user avatar
  • 35.6k
5 votes

What are some examples of non-homologous sequences having similar functions?

Serine Protease Catalytic Triad This is classic example of convergent evolution in catalytic mechanisms. Shown below are chymotrypsin (4CHA, green) and subtilisin (1ST2, blue) aligned on their ...
canadianer's user avatar
  • 17.8k
3 votes
Accepted

What is the sequence similarity between humans and chimps in the noncoding genome?

According to "MUMmer4: A fast and versatile genome alignment system" (Plos Computational Biology 2018): "First we aligned the current assemblies of human and chimpanzee, using the ...
arara's user avatar
  • 706
3 votes
Accepted

Is it possible for a sex chromosome to be homologous?

How can a male fly be pure-breeding? A fly or any organism can only be pure-breeding for a certain trait, not all traits at once. If the trait-determinant allele is found on an autosomal chromosome, ...
S Pr's user avatar
  • 6,262
3 votes

Gene vs Protein homology

In most* scenarios you will probably want to look at a comparison of proteins following some additional matching that considers more than a single gene/protein. Luckily, this is a very common problem ...
tsttst's user avatar
  • 1,597
3 votes
Accepted

Does homology of a trait necessarily imply that the most recent common ancestor had the trait?

Yes, assuming you treat the term strictly. The term homologous implies that the most recent common ancestor had the trait, although it would be possible for the term to be used in error, when ...
Bryan Krause's user avatar
  • 46k
2 votes

The pectoral fins of a whale and a shark. Are they analogous organs?

The ancestors of all jawed animals probably had pectoral fins [Ref]. This primitive feature is homologous to shark pectoral fins (fig. 1). The forelimbs of quadrupeds are evolved from the pectoral ...
JCThomas's user avatar
  • 149
2 votes

The pectoral fins of a whale and a shark. Are they analogous organs?

They are analogous at to function. Whales derive from terresterial animals that "returned" to the sea. Evolution adapted the forearms to fins. Here's a great diagram: http://evolution.berkeley.edu/...
bpedit's user avatar
  • 1,351
2 votes

What are some examples of non-homologous sequences having similar functions?

Hoxd12 and Hoxd13 are involved in the development of wings in birds (Vargas and Fallon 2004). pdm and aptorus are involved in the development of wings in insects (Williams et al. 1993, Averof and ...
Remi.b's user avatar
  • 68.1k
2 votes

Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits?

This vocabulary is common in textbook but not in the peer-reviewed literature First please note that while those terms are often used in intro class to evolutionary biology, they are actually rarely ...
Remi.b's user avatar
  • 68.1k
2 votes

Is it possible for a sex chromosome to be homologous?

To add to @S Pr's answer and provide another cool and useful fact, in some organisms, like birds, the males are the homomorphic sex (their sex chromosomes are the same size and haven't decayed like ...
CheapWill's user avatar
2 votes

Is it rare for a virus to be similar to its host?

Phage similarity to host Briefly, yes. Generally speaking phage have relatively similar compositional features (e.g. k-mer frequency, see linked paper) and also direct homology (large regions of ...
Maximilian Press's user avatar
2 votes
Accepted

is there an assumption of homology?

I canĀ“t remember to have heard of an "assumption of homology"; i studied (evolutionary) biology in Germany for several years. If I understand correctly, you are wondering how to tell ...
nika's user avatar
  • 189
1 vote

Sequence homology of cytokeratins

Going through the quote: Sequence homology of cytokeratins is very high, There are many human cytokeratin genes and corresponding proteins, and they have very similar sequences of amino acids. but ...
mgkrebbs's user avatar
  • 9,054
1 vote
Accepted

Does the minimum spanning tree tell us anything useful about evolutionary ancestry?

Your graphic is omitting nodes of the tree, branching points, which are essential for trees and phylogeny. When you read the data file, you should count the brackets ((( ))) because they signify ...
bandybabboon's user avatar
  • 10.4k
1 vote

Gene copies vs. gene paralogs - what's the difference?

The general term "copies" has multiple meaning with reference to genes. In diploid organisms for example, we have two copies of each gene (except those on the Y chromosome). However, these copies are ...
Karl Kjer's user avatar
  • 7,663
1 vote
Accepted

tissue-specific expression of homolog genes

The evolution of new genes is frequently associated with gene duplication. The paralogous genes are then free to evolve on their own into new functions over time. Sometimes (usually) the paralog will ...
Karl Kjer's user avatar
  • 7,663
1 vote
Accepted

Finding phylogenetic distance between sequences?

No, because it is really not a binary decision. There are attempts to associate percent pairwise difference with taxonomic ranks (particularly species), but this is problematic because every ...
Karl Kjer's user avatar
  • 7,663
1 vote

Identity and similarity for Multiple Sequence Alignment (MSA) of proteins

I've never used T-Coffee but it looks like the web-server version gives you a total score as well as a score for each individual sequence; do you know if those numbers are related to the numerical ...
Slavatron's user avatar
  • 1,010
1 vote
Accepted

NCBI EUtils. Get Homolog infromation using Gene ID

From Entrez Programming Utilities Help [Internet]: Input: Any Entrez text query (&term); Entrez database (&db); &usehistory=y; Existing web environment (&WebEnv) from a prior E-...
James's user avatar
  • 11.3k

Only top scored, non community-wiki answers of a minimum length are eligible