A web-service on insufficiently identified fungal ITS sequences

emerencia is a tool designed to monitor the identity of insufficiently identified fungal ITS sequences in Genbank. It does this by keeping a fresh local copy of all fungal Genbank ITS sequences and dividing them into two categories based on their Genbank annotation: identified and insufficiently identified. All insufficiently identified sequences are, twice a week, BLASTed against all identified sequences and the best BLAST matches and their identities are stored. In addition, all insufficiently identified sequences are also BLASTed against all other insufficiently identified sequences. emerencia can be queried in a number of ways: for your favourite accession numbers of insufficiently identified sequences, for publications where insufficiently identified sequences were made use of, for insufficiently identified sequences that have a given identified sequence as their best BLAST match, and for all insufficiently identified sequences (and their best BLAST matches) that match a set of key words. emerencia now also features a new search function that allows you to search for all insufficiently identified sequences associated with any user-specified genus of fungi.

If you use emerencia in your research, please consider citing the original publication (Nilsson et al 2005).
The new search function is described in more detail in a separate publication (Ryberg et al 2009).

Check accession number of insufficiently identified sequence
Please provide the accession number of the insufficiently identified sequence you wish to check. You can only type in one accession number at the time. Some examples: AF477002, U65598, AF422940.

Accession number   

Check specific publication for insufficiently identified sequences and their identity
This function assumes you to have a literature reference the insufficiently identified sequences of which you wish to know more about. Please provide that literature reference as at least five but at most ten key words (in any order). For example, for literature reference Zhang,W., Wendel,J.F. and Clark,L.G. Bamboozled again! Inadvertent isolation of fungal rDNA sequences from bamboos (Poaceae: Bambusoideae) Mol. Phylogenet. Evol. 8 (2), 205-217 (1997) you could type Zhang Wendel Clark Bamboozled again or 1997 Poaceae Clark Inadvertent isolation. Note that only alphanumeric characters (aA-zZ and 0-9) are allowed, that a key word must consist of two or more characters, that all key words must be mutually exclusive (non-identical), and that at least five - but not more than ten - key words have to be specified. The more specific your key words are, the less redundancy you will see.

Literature key words   

Check identified accession number for insufficiently identified matches
This function lets you check whether an accession number of an identified sequence is the best BLAST match of any insufficiently identified sequence in the database. Provide one - and only one - accession number as input. Some examples: AY394921 and AY394907.

Accession number of identified sequence   

Search for insufficiently identified sequences and their best matches
This function lets you provide two to five key words. These will be used as query against the species annotation of the insufficiently identified sequences. Insufficiently identified sequences that match these criteria will be shown together with their best BLAST matches. Note that you will have to specify two to five key words of at least two alphabetical (aA-zZ) characters each. Some examples: Amanita sp, uncultured marine ascomycete, Woollsia root associated fungus.

Search string   

New search function!
List all insufficiently identified sequences that belong to a user-specified genus
This function will list, for any user-specified fungal genus, all insufficiently identified sequences whose best BLAST match is annotated as belonging to the genus in question. The results are presented in four sections: i) detailed information on all sequences matched by the above criteria, ii) the number of such sequences broken down to study of origin, iii) the corresponding identified sequences broken down to study of origin, and iv) the insufficiently identified sequences grouped by distinct species. A list of all genera matching at least one insufficiently identified sequence can be found here. Some examples of query genera: Boletus, Amanita, and Craterellus.

Genus name   
Use the whole ITS region   Use only ITS2                

emerencia relies on our being able to distinguish identified sequences from insufficiently identified ones.

Maintained by Henrik Nilsson at Goteborg University
Logotype graciously provided by Klas Benjaminsson at Bomb Mediaproduktion