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Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W267-72.

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.

Author information

  • 1Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. kiyoko@kuicr.kyoto-u.ac.jp

Abstract

KCaM (KEGG Carbohydrate Matcher) is a tool for the analysis of carbohydrate sugar chains, or glycans. It consists of a web-based graphical user interface that allows users to enter glycans easily with the mouse. The glycan structure is then transformed into our KCF (KEGG Chemical Function) file format and sent to our program which implements an efficient tree-structure alignment algorithm, similar to sequence alignment algorithms but for branched tree structures. Users can also retrieve glycan tree structures in KCF format from their local computers for visualization over the web. The tree-matching algorithm provides several options for performing different types of tree-matching procedures on glycans. These options consist of whether to incorporate gaps in a match, whether to take the linkage information into consideration and local versus global alignment. The results of this program are returned as a list of glycan structures in order of similarity based on these options. The actual alignment can be viewed graphically, and the annotation information can also be viewed easily since all this information is linked with KEGG's comprehensive suite of genomic data. Analogously to BLAST, users are thus able to compare glycan structures of interest with glycans from different glycan databases using a variety of tree-alignment options. KCaM is currently available at http://glycan.genome.ad.jp.

PMID:
15215393
[PubMed - indexed for MEDLINE]
PMCID:
PMC441611
Free PMC Article

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