Table 1

Functions of the emerencia web-service. Functions of the emerencia web-service at http://emerencia.math.chalmers.se webcite; some examples and an informal walkthrough are also given at this address. The output of the functions features relayed hyperlinks to GenBank, Google, and Tree of Life for quick retrieval of additional information; where applicable, insufficiently identified sequences are also hyperlinked to the SEARCH FOR INSUFFICIENTLY IDENTIFIED SEQUENCE BY ACCESSION NUMBER function for a more detailed description of the sequence and its matches.

SEARCH FOR INSUFFICIENTLY IDENTIFIED SEQUENCE BY ACCESSION NUMBER

For any given accession number of an insufficiently identified sequence, this function shows the present and previous best BLAST matches from the table of identified sequences together with match scores and relevant annotation. A Clustal W multiple alignment [34] of the sequences is generated and shown as an important aid in interpreting the BLAST match values. In addition, all the above is shown for the present and previous best BLAST matches in the table of insufficiently identified sequences. This function requires that the accession number provided by the user be present in the table of insufficiently identified sequences.

CHECK SPECIFIC PUBLICATION FOR INSUFFICIENTLY IDENTIFIED SEQUENCES AND THEIR IDENTITY

This function retrieves all insufficiently identified sequences stemming from the user-specified publication and shows the present best identified BLAST match (and some additional information) for those sequences. The function expects 5–10 distinct key words from the title / author /journal fields of the publication and requires that at least one insufficiently identified sequence was released together with the publication in question.

SEARCH FOR INSUFFICIENTLY IDENTIFIED SEQUENCES MATCHING ACCESSION NUMBER OF IDENTIFIED TAXA

For any given accession number in the table of identified sequences, this function retrieves and details all entries in the table of insufficiently identified sequences for which this accession number represents the best BLAST match. It requires that the specified accession number be present in the table of identified sequences and will proceed only if that accession number indeed constitutes the best BLAST match of at least one insufficiently identified sequence.

SEARCH FOR INSUFFICIENTLY IDENTIFIED SEQUENCES BY KEY WORD

This function lets the user query the species annotation field of the table of insufficiently identified sequences using 2–5 key words, and displays all insufficiently identified sequences matching the key words. For those sequences, the best BLAST match to the table of identified sequences will be shown together with some additional information.


Nilsson et al. BMC Bioinformatics 2005 6:178   doi:10.1186/1471-2105-6-178

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