Difference in BLAST and eggNOG

Question

[Shaurya]

I am a freshman at college and I am a working on an evolutionary biology of eukaryotic cells project. I have come across two different sets of methods in the papers I read. One is BLAST and one is eggNOG. From what I have learnt BLAST is basically used to find segments of matches between the query an the source by using W substrings of nucleotides, expanding their neighborhood up to some set limit and then searching in a hashed database. I have not come across eggNOG before. The Wikipedia page says it is maintained by EMBL and has clusters of orthologous groups. Besides this I have no information about the differences in the two. I also plan to use Hidden Markov Models during genome alignment and I shall eventually be using this information to construct phylogenetic trees to infer changes. I have a list of proteins which I shall be searching.

Could someone please help me out by telling the differences between the two ? And would using HMMs really make a difference ? I would be implementing the HMMs from scratch mostly as I have not found tools that do that like BLAST or eggNOG.

I am currently learning relevant parts of computational biology from an online course so this is the reason that I have this doubt. I would be very grateful for any help that you could provide.

[Ram]

Cross-posted on bioinfo SE https://bioinformatics.stackexchange.com/questions/16238/difference-in-blast-and-eggnog

Do not create the same post on multiple forums - that is bad etiquette.

[Shaurya]

sorry its just that I did not get an answer there yet and I would like to know this as soon as possible. Should i delete the post from here?

[Ram]

You should have mentioned this in your post. No online forum can guarantee a quick response - remember that you're asking a group of volunteers and not contacting customer support on a service you're paying for.

Plus, you've posted the question on a weekend and waited less than 12 hours before deciding you've waited long enough. That comes across as quite self-important.

Answer 1

[andres.firrincieli]

I have not come across eggNOG before. The Wikipedia page says it is maintained by EMBL and has clusters of orthologous groups. Besides this I have no information about the differences in the two. I also plan to use Hidden Markov Models during genome alignment and I shall eventually be using this information to construct phylogenetic trees to infer changes.

I think you should start reading the eggNOG-mapper preprint.

Could someone please help me out by telling the differences between the two (BLAST vs eggNOG) ? And would using HMMs really make a difference ? I would be implementing the HMMs from scratch mostly as I have not found tools that do that like BLAST or eggNOG.

BLAST and eggNOG are not tools for HMMs searches. eggNOG is the database, while eggNOG-mapper is the pipeline used to assign your proteins to clusters of orthologous groups. eggNOG-mapper can query two different databases: 1) a protein database via Diamond-BLASTP/BLASTX or mmseqs2; 2) a database of HMM profiles via hmmscan. Therefore, the real question is:

Difference in BLAST and HMMER

[Shaurya]

okay thank you that answers my question. I don't see an option to accept this answer like on stack exchange but my query has been resolved completely.

[Ram]

That's because it's a comment and not an answer. I'll move it to an answer, and then you should see a green check mark similar to Stack Exchange that you can use to accept the answer.

EDIT: Shaurya I've moved the post to an answer now, you should be able to accept it.