Hydrophobicity is usually analyzed by averaging over a fairly long window e. All of the parameters analyzed in this utility are plotted in the sequence viewer above the sequences. The parameters are usually calculated for all active sequences and the plot is aligned to the sequence so there may be gaps in the plot where there are gaps in the sequence alignment.
If you exit the Prediction Utility , enter the Align and Superpose utility, and uses any of the tools there to change the sequence alignment then, where appropriate, the plot will be updated to keep in sync with the sequence. The hydrophobicity plot might be a useful in alignment as, generally, the hydrophobicity plots of two homologous structures are strongly correlated. The plot legends are colored the same as the plot that they identify.
By picking a plot legend you can toggle on or off the display of the plot. The legend for an undisplayed plot is colored gray. To change the display status of several plots it may be quicker to pick the plot title at the top of the legend and a selection dialog box is presented. To toggle on or off the display of all plots pick the G icon on the bottom left of the sequence viewer.
The secondary structure prediction tools are applied to all active sequences and the sequences recolored according to their predicted secondary structure. The secondary structure propensities for one sequence will be plotted in the Sequence Viewer. If there is more than one sequence active, then you are prompted to select one sequence for which propensities are plotted. This tool plots the hydrophobic profile for the active molecules. This opens the Hydrophobic Profile Options dialog box.
You can change the hydrophobicity scale and the window length used in the hydrophobicity plot. The window length for the conservation plot is also changeable.
The options in this dialog allow you to select different scales, residue window lengths, molecules, drawing averages, and difference profiles. This tool plots the conservation profile for two or more active molecules. The conservation profile is a measure of the extent of sequence conservation along two or more aligned sequences.
Sequences must first be aligned. A high conservation number is given when similar chemical types of amino acid occur at a position, and a lower number is given when chemical types differ. Conservation profiles can be averaged over a window - the length can be changed via the Profile Options tool.
This plots a graph in the sequence viewer showing, for each column of residues in the sequence viewer, the number of residues which fit into a given chemical classification such as acidic or aromatic. Inactive sequences are excluded from this analysis. The plot shows ten different classifications and may be difficult to interpret when all classifications are displayed simultaneously.
You can toggle off or on the display of a given classification by picking its name on the plot legend. To change the display status of multiple classifications pick the legend title Composition and you will be presented with a dialog box. This tool performs a Momany secondary structure prediction for each active sequences and recolors the sequences according to the predicted secondary structure.
The prediction propensities for one sequences are plotted in the sequence viewer. This tool performs a GOR prediction based on all the currently active sequences. To get meaningful results the sequences must be aligned. The prediction propensities are plotted to the sequence viewer. When pasting in a sequence do not add any comment or description lines, but spaces and carriage returns are allowed.
You can also upload single sequences as files. Select a plain text file with one or more sequences in a supported file format. JPred accepts five types of input link to format examples. Batch submission of multiple sequences for individual secondary structure prediction could be done using a file in FASTA format see link to an example above and each sequence must be given a unique name up to 25 characters with no spaces.
Additional words or descriptions on the defline will be ignored. Batch jobs cannot be run interactively and results will be provided via e-mail only. A limit of sequences are allowed per batch submission. You may submit several batch jobs, but there is a hard limit of 4, sequence predictions in total per user per day.
Please let us know if this limit is a problem for you and we'll look at temporarily changing it. This is referred to as the "hotdogs and surf board" model in the chat, where the hotdogs are the helixes and the surfboard is the sheets. In designs of this type, the sheets on the outer edge of the surfboard tend to have a lot of hydrophobic residues on both the "outer" and "inner" helix-facing sides.
The prediction services seem to have difficulty guessing that these hydrophobic sequences form sheets. Here is the veteran chat that discussed all these tools. The chat has be lightly edited to remove some interspersed conversations and correct a few typos. Generated by irclog2html. ISBN You'd have to know Vigata to get the rest. Foldit Wiki Explore. Recent blog posts Forum.
Most visited. Explore Wikis Community Central. Register Don't have an account? Secondary structure prediction tools. Edit source History Talk 0.
Cancel Save. Fan Feed 1 Campaign 2 Hydropathy index 3 Protein backbone. Universal Conquest Wiki. I don't know for certain but I've speculated that the predictions might be only there as a hint but aren't always in the right place; thus, might need to be moved somewhere else.
I always check jpred as a point of comparison, though it has the same weakness on all-blue areas. Loci has a nice script called AA Edit that will let you put the sequence in the clipboard. I think in the previous puzzle the predictor got confuzed by the leucines and arginines which are more often found on helices than on sheets.
Kabubi -- I may just be a hack, but sometimes I just change things and ignore predictions You can also copy and paste the AA sequence from the puzzle notes For the heck of it I ran the B-Turn predictor Wonder how long that'll take haha. I'm quite possibly the furthest thing from a BioChemist, Chemist, or anything even remotely close to anyting in any scientific field.
But it does help.
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