Blast: Homology Or Similarity?

Question

[Whetting]

Hi Biostars,
I am having a dispute with a reviewer. Is BLAST a Homology or similarity based search?
thanks
EDIT
The BLAST is performed against a custom DB containing only homologous proteins.

[Manu Prestat]

The fact the your blast DB is built form homologous sequences does't change anything to answer your question. The only thing that BLAST can tell you is that your 2 (as it's pairwise alignment) sequences are similar, and the more similar they are, the less the probability you're wrong by assuming it's because those are homologs.

Answer 1

[Rm]

Blast is "Similarity" Based Search: Homology might be implied from the Similarity. In biological context Homology is derived from common ancestry.

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

[Ketil]

To elaborate, two sequences can be similar without being homologous, for instance binding sites for proteins can have selection pressures towards the same pattern. BLAST has no way to tell these similarities apart from similarities caused by shared ancestry.

[Rm]

...Convergent evolution

Answer 2

[swbarnes2]

Homology is a conclusion of evolutionary relatedness. Sequence similiarity is a piece of data that would allow one to conclude homology.

BLAST might tell me that a bit of DNA is highly similar between a vector and an unfinished genome. But I'd be wrong to conclude homology from that!

Answer 3

[natasha.sernova]

statistically significant similarity implies homology

See the paper below:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820096/

An Introduction to Sequence Similarity (“Homology”) Searching

William R. Pearson