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.
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.
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?
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.