1. There are several database containing nifH sequences like fungene (19500 seq), arb database (32,954 seq), zehr (72000 seq) and farnelid (5,00,000 seq). what is the difference between these databases ?
2. Can fungene pipeline be used for taxonomic classification of nifH functional gene ?
3. Any other pipeline/tool available for taxonomic classification of nifH gene ?
Well you have yourself mentioned the differences among the databases in parenthesis. Different databases have been published in different years with different functionality, thus there are differences.
But, only the large number of sequences is not a criteria of good database.
However, JZehr lab has and maintain a very good ARB formatted database. It is also widely used and I could recommend it if you are comfortable with ARB software.
And there are several pipelines, new pipelines might have new algorithms so could be used with ease. As this recent semi automated pipeline. You can give it a try.
Article Evaluation of Primers Targeting the Diazotroph Functional Ge...
In addition to the pipeline mentioned above (Article Evaluation of Primers Targeting the Diazotroph Functional Ge...
), you can also have a look at this one:Article Diazotroph Community Characterization via a High-Throughput ...
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