16S rRNA phylogenetic analysis - stuck!!!!! (May/06/2006 )
Hi there alll,
First of all thanks for the RE digest. It worked out wonderfully. Another question that i have is that my blast results shows alot of bacteria with similar homology percentages. Since im trying to create a phylogenetic tree, can i count in all the bacteria or for each sequence only one bacteria should be included in the tree. Im confused.
My supervisor wants me to have at least 200 sequences. But for each sequence i get a hit of 3-6 bacteria of different species diversity. This can minimise my work load alot if i can include all the bacteria into my tree.
Pls advice. Im stuck here!!!
Thank you again.
I am not to perfectly clear on phylogenetics (although I am learning!), but I think you select the type strain sequence. Each organism should have a type strain that has been verified but multiple methods (ie. DNA:DNA hybridzation, 16S, biochemical tests) of being what it is. These guys are published in the International Journal of Systematic Microbiology and you can obtain the bacteria from strain collections like ACCC or DSMZ. So basically, you need to go to the literature and research what the type strains are and then fish out the sequence from the database. If you are looking at a particular group, for example the Enterobactericeae family, I would be surprised that someone out there hasn't already done it. You could find their paper and see what sequences they used.
Anyway thanks for the advice. Im actually tryimh to fish out all the 16S diversity in antarctic soil from a particular site. So im confused whether shall i include all the same homology into the phylogenetic tree.
well, you have not mentiioned your problem very clearly. But I am suggesting based on what I understand form your post . You should include all the possible sequeces from a given location into phylogentic tree but more than 100 may look too much crouded. As the no of seq increase the confidence level of the programme also increase, I mean it will give a better stastical result. If you have two or more sequences which are 100% similar , there is no point in putting all of them, but if you put many closely related sp with some moderatley and some distatnly related sp in yoiur tree , you will get a better phylogentic tree.