I'm battling to decide on the best site/database to use for blasting sequences from fungal species. I'm currently unsure whether Mycobank, FungiDB, or NCBI is better. It seems that NCBI separates out genera better than the other two, but also seems to be lacking in genera in the linked DB. I'm trying to minimize the need to build phylogenetic trees as much as possible to assist in species identification. Can anyone advise?
I advice not to eliminate the multiple sequence alignment and phylogenetic tree construction. Blasting (unless its a custom blast) consider all the sequences whats available to show the similarity. On the other hand multiple sequence alignment which takes input of your 'selected' sequences to access the sequence similarity and phylogenetic tree will represent the relationship between those selected sequences. Bypassing these crucial step will just make your result less credible.
Thanks Abhijeet, I just wanted to make sure that there isn't something that I could be missing that at least eliminated a large chunk of the suggested genera. But will build raxml trees to separate out the possibilities.
Out of interest, which is your go-to database for Fungi species?
I guess NCBI is pretty sufficient as all the sequences are eventually available in it. I have not use the fungal databases, so I am not aware how good they are. But you can use all the databases for the data retrieval and make collective and manual analysis which will suit more of your need. Multiple sequence alignment with MAFFT and regroup flag is recommended, you can decide the number of bootstraps. See for the abnormal groups in aligned file and curate. Use FastTree for making tree, its fast and reasonably accurate. Raxml tree can take very long time for a large dataset.
http://fungi.ensembl.org/index.html
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/fungi/
Hi Ashadee Kay Miller,
Use https:/www.catalogueoflife.org/col/info/databases although I've used NCBI, UNITE and other databases as well, but I didn't get
my target data, the last one I used life catalog DB, that gives me a better result.
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