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http://stanxterm.aecom.yu.edu/wiki/index.php?page=Protein_domains_a...
PROSITE - http://www.expasy.ch/prosite/ SMART - http://smart.embl-heidelberg.de/ To search an integrated database, use one of these links CDD - http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml InterPro - http://www.ebi.ac.uk/interpro/ Uniprot - http://www.pir.uniprot.org/search/SearchTools.shtml best as it provides almost all the known information on the protein on one page To search for consensus sites (phosphorylation, glycosylation, etc.), use ELM server - http://elm.eu.org/ (multiple) CBS server - http://www.cbs.dtu.dk/services/ - kinase-specific phosphorylation site prediction, glycosylation prediction, sorting motifs, etc. Identifying UNKNOWN or specific repeats, motifs and domains in your sequence of interest This involves, first, collecting a group of sequences that are similar to yours. The set of sequences (or their alignment) is then analyzed for patterns. Some online servers are PRATT - for patterns - http://www.ebi.ac.uk/pratt/ RADAR - for repeats (using single sequence) - http://www.ebi.ac.uk/Radar/ To look for a pattern designated by you in a sequence, use the protein pattern find tool at http://bioinformatics.org /sms2/protein_pattern.html
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