PRALINE output examples

♦ SOAP service ( WSDL) now available. PRALINE sample output References and FAQs PRALINE is a multiple sequence alignment program with many options to optimise the information for each of the input sequences; e.g. homology-extended alignment, predicted secondary structure and/or transmembrane structure information and iteration capabilities.

The following examples are samples of the possible outputs of the PRALINE Server using the different available strategies. In the first 7 examples, the sequence set used consists of 12 Cytochrome P450 proteins compiled together in the HOMSTRAD structure alignment database. PSIPRED (Jones, 1999) is used in all examples for consistency, but the results are equivalent to the other prediction methods available. Cytochrome P450 is a family of the body's more powerful detox enzymes. Over 60 key forms are known, with hundreds of genetic variations possible, producing a wide variety of susceptibility to specific toxins. Problems with P450 are often involved in porphyria type disorders. P450 production may be inhibited or substantially used up by H2 blockers, some antacids, SSRI's (Prozac, Paxil, Zoloft, etc.) and perhaps one fifth of all medications. In this manner, these drugs have the potential to worsen, or even create, a susceptibility to many common chemicals, and thus may trigger Multiple Chemical Sensitivities / Environmental Illness and related syndromes. For more information and useful links about Cytochrome P450 proteins please start from here. • Example 1: PRALINE output using global (standard) progressive alignment. The tree and custom colour scheme options have been activated. • Example 2: PRALINE output using pre-profile global processing with no iteration and a cut-off of zero. The tree and custom colour scheme options have been activated. • Example 3: PRALINE output using pre-profile global processing with 5 iteration and a cut-off of zero. The tree and custom colour scheme options have been activated. • Example 4: PRALINE output using pre-profile global processing with no iteration and a cut-off of zero and integrated secondary structure information from the prediction with PSIPRED (Jones, 1999), no iteration and a cut-off of zero. The tree and custom colour scheme options have been activated. • Example 5: PRALINE output using the homology-extended strategy. The tree and custom colour scheme options have been activated. • Example 6: PRALINE output using the homology-extended strategy with integrated secondary structure information from the prediction with PSIPRED (Jones, 1999). The tree and custom colour scheme options have been activated. • Example 7: PRALINE output using the homology-extended strategy with integrated secondary structure information from both DSSP and the predictions of PSIPRED (Jones, 1999). Note that here DSSP overides PSIPRED. The tree and custom colour scheme options have been activated. In the following 3 examples the sequence set used consists of 14 proteins belonging to the MscL family of Large-conductance mechanosensitive channels compiled together in the BAliBASE multiple alignment database. In all examples transmembrane structure prediction is performed by PHOBIUS (Käll, 2005) is used for consistency, while PSIPRED (Jones, 1999) is the method of choice for secondary structure prediction. The mechanosensitive channel of large conductance (MscL) belongs to a family of transmembrane channel proteins in bacteria and functions as a safety valve that relieves the turgor pressure produced by osmotic downshock. MscL gating can be triggered solely by stretching of the membrane. This text and more information on the MscL transmembrane proteins and channeling mechanisms can be found in Jeon J. and Voth G.A. (2008), Biophys. J. 94(9):3497-3511. • Example 8: PRALINE output using the homology-extended strategy with integrated transmembrane structure information from the predictions of PHOBIUS (Käll, 2005). The tree and custom colour scheme options have been activated. • Example 9: PRALINE output using the homology-extended strategy with both integrated transmembrane and secondary structure information from the predictions of PHOBIUS (Käll, 2005) and PSIPRED (Jones, 1999), respectively. The tree and custom colour scheme options have been activated. • Example 10: PRALINE output using the homology-extended strategy with both integrated transmembrane and secondary structure information from the predictions of PHOBIUS (Käll, 2005), DSSP and the predictions of PSIPRED (Jones, 1999). Note that here DSSP overides PSIPRED. The tree and custom colour scheme options have been activated.