Ises, list sequence alignment

To search amino acid sequence against the BLOCKS database at http // www.blocks.fhcrc.org/, select Block Searcher to open the search form. Choose the options, paste the query sequence, and click the Perform Search button. The search returns lists of matched blocks (I.D. descriptions, number of blocks, and combined E values), locations (amino acid positions of individual blocks and its E value), and pairwise alignment of the blocks with the matched query sequences (Figure 12.17). 

The 3D-1D compatibility algorithm (Ito et ai, 1997) is applied to predict the secondary structures by threading at SSThread of DDBJ (http //www.ddbj.nig.ac.jp/E-mail/ ssthread/www service.html). The threading result reports the anuno acid sequence with the predicted secondary structures (H for a-helix E for -strand and C for coil or other). The threading prediction of the query sequence against the structural library chosen from PDB at LIBRA I (http //www.ddbj.nig.ac.jp/E-mail/libra/LIBRA I.html) reports a list of compatible structures and 3D-ID alignment results recording the secondary structures and accessibility. 

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