I have a sequence of a (putative) glycoside hydrolase enzyme , I want to do a phylogenetic analysis to get information about its class and anticipated activity. Which online server can do this task?
Thanks in advance
Hi Yasser,
some (very) basic suggestions.
1) Run a search exploiting as a template (query) your protein sequence against the non-redundant (nr) protein sequences database. You can use BLAST available at NCBI:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
2) if you find some significant homology to other proteins, first of all you can then check if they are indeed catalogued/reported as glycoside hydrolases
3) in case you have some success, you can start to collect and play with these sequences and you may start to build a multiple alignment. For example, you may want to use MUSCLE:
http://www.ebi.ac.uk/Tools/msa/muscle/
or you could also even try to start building up multiple alignments and some phylogeny trees using:
http://phylogeny.lirmm.fr/phylo_cgi/index.cgi
Hope this can give you some initial help. Good luck.
a.
In addition, the use of a "server" is usually justified by the amount of data that you are analyzing (e.g. model complexity, number of sequences and alignment length). If you end up with not so many data you may even be able to use your own desktop computer. After you've explored the options mention by Dr. Brancaccio, check out RAxML, which is a routinely used software for maximum-likelihood phylogenetics.
Cheers,
http://sco.h-its.org/exelixis/software.html
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