By Kiyoko F. Aoki-Kinoshita
This publication offers glycoscientists with a instruction manual of valuable databases that may be utilized to glycoscience study. even though many databases are actually publicly on hand, one of many hurdles for his or her clients is the educational curve required to successfully make the most of these databases. accordingly, this publication not just describes the prevailing databases, but in addition presents how one can receive the objective facts. that's, simply because many databases supply quite a few info which may be received from diverse views, each one bankruptcy offers clients with power organic questions that may be replied by way of a specific database and step by step directions, with figures, on easy methods to receive that info. Troubleshooting suggestions also are supplied to help clients encountering difficulties that may be envisioned while utilizing those databases. in addition, touch info for every database is equipped in case unforeseen concerns arise.
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Extra info for A Practical Guide to Using Glycomics Databases
Shinmachi et al. 1 Introduction As the third major molecule of biopolymers next to DNA and proteins, glycans have been found to be involved in various important biological functions. The structure of glycans, however, differs greatly from DNA and proteins in that they are branched, as opposed to linear sequences of amino acids or nucleotides. Therefore, the storage of glycan information in databases, let alone their curation, has been a difficult problem. This has caused efforts in the integration of glycan data between different databases difficult, making an international repository for glycan structures, where unique accession numbers are assigned to every identified glycan structure, necessary.
2002) defines a one-letter code to represent monosaccharide residue types. The LinearCode® approach requires a dictionary table where residue names are explicitly defined. Therefore, only glycan structures that consist of residues that are listed in the dictionary can be encoded with LinearCode®, and the user needs to know the definitions to be able to interpret glycan structures encoded in this format because the codes do not resemble IUPAC nomenclature. On the other hand, this clearly defined dictionary produces nonambiguous names and is significantly less error-prone than formats such as CarbBank notation or LINUCS that allow free-text residue definitions.
The same confirmation page as used in the “Graphical Interface” registration process will be displayed. 4 Registration Results The “Graphical Input,” “Text Input,” and “File Upload” registration procedures all provide a confirmation page after structure input. Once confirmed, the list of glycan structures with their unique accession numbers is displayed (Fig. 7). For each glycan structure, the theoretical mass is computed along with the structure in WURCS format. Such automatically computed data can be confirmed on the glycan entry page containing the detailed information for each glycan structure.
A Practical Guide to Using Glycomics Databases by Kiyoko F. Aoki-Kinoshita