Hello,
Greetings.I am aware of tools like Vikodak, PiCrust,Tax4Fun etc for prediction of functional potential from 16S rRNA genes of bacterial communities.In my current study, I also checked for fungal community structure and diversity targeting internal transcribed spacer (ITS) region using ITS3 and ITS4 primer combination.
So, I am interested to know is there any similar tool for analyzing functional potential for Fungi?
Looking forward for some suggestions.
Thanks,
Sandipan
I think, there are other tools like Geo-Chip 3.0, FUNGIpath, Fungi DB, MatInd and Mat Inspector etc. Please have a look of the attached file that may help you.
Hello,
you may try this approach:
Article FUNGuild: An open annotation tool for parsing fungal communi...
Follow this link
Article A Review of Bioinformatics Tools for Bio-Prospecting from Me...
regards
Assigning a "lifestyle" or "trophic mode" to a fungus is typically much harder than for a prokaryote. These trophic modes are not conserved even within genera, and mycologists can argue endlessly about assigning a role to a particular genus or species (is Fusarium a saprotroph, a pathogen or an endophyte)? This is one of the reasons that eukaryotic metabarcoding lags so far behind prokaryotic metabarcoding.
In addition to what Tyler Bourret pointed out, there is an increasing body of literature that the ITS region(s) vary in their utility for identification of a large number of fungi (see some of the previous discussions elsewhere on ResearchGate such as https://www.researchgate.net/post/What_primer_sets_are_good_for_fungal_community_profiling_by_pyrosequencing) and that multilocus methods are much better for many important and diverse groups of fungi (e.g. http://www.westerdijkinstitute.nl/fusarium/). In addition, there are numerous errors in the identifications and classifications associated with ITS in some of the major databases (e.g. DOI 10.1007/s13225-014-0291-8, doi.org/10.1101/288654, etc.) as well as database biases (e.g. http://geoffreyzahn.com/limitations-of-the-unite-fungal-database/). These types of complications and errors make assigning a functional prediction based on ITS difficult and such assignments questionable.
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