This topic is locked from further discussion. Separate letter groups using "-", e. While there is no check that you have done this because MEME runs as a separate program other than that the sequence names need to match, as do the number of sites , using a primary set different to the sequence set MEME searches is unlikely to be useful. View repository View change log Browse repository tip files Download as a. It takes two files as input—the sequence file to be input to MEME, the "primary" file and a "control" sequence file of sequences believed not to contain the same motifs as in the "primary" file.
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I think this thing has a little bit of life left in it. Only the given strand is considered. Consider both strands when calculating position specific priors for alphabets - select 'Yes' to consider both strands when calculating PSPs for complementable alphabets or 'No to consider only the given strand.
No extra information is reported. If you only psspgen one of scalemin or scalemaxthe other is calculated as described in Options.
How much longer will the PSP gen last?
Any letters in sequence representing ambiguous bases or amino acids result in a word w -mer containing that word or triple in the case of protein being counted whether in the primary or control sets as if it occurred once, to minimize its score.
The maximum width is set to When using the -triples option, only consider triples starting at the start pspyen the site. In spaced triples mode, psp-gen scores a site on the basis of the spaced triple fitting the w -wide word at that site that has the highest score.
Use spaced triples instead of whole-word matches - use spaced triples instead of whole-word matches recommended when using the protein alphabet.
An option that only applies to triples is -fixedstartwhich only allows triples for the current site under consideration that start at the beginning of the site. Mormaso Follow Forum Posts: The PSP has at least a good three pspggen four years left in it, and an impressive library of games already to boot.
For more detail, see Options. PSP calculation starts from the following equation based on the D -prior described in the Narlikar et al. Send to standard error primary pspgem control file names, min and max scores and min and max widths, tab-separated. When using the -triples option, only consider triples starting at the start of the site. Any sequence of letter that appears together should be matched as equal. An option that only applies to triples is -fixedstartwhich only allows triples for the current site under consideration that start at the beginning of the site.
We repeat scoring for the whole range of motif widths under consideration, and choose a "best" width using one of two methods: Set the lowest score value after scaling - select 'Yes' to set the lowest score to 0.
Abgoj Follow Forum Posts: Use these position-specific priors in MEME: Any sequences not in the PSP file are given a uniform prior probability. Do not report scores to standard error. I certify that I am not using this tool for commercial purposes.: This topic is locked from further discussion.
How much longer will the PSP gen last? - PlayStation Nation - GameSpot
This variant is useful in data sets where a high number of sites achieve similar high scores more likely to happen with protein sequences. See Variations below for more details on triples and choosing the "best" width.
Once we have scored all sites for a given value of wwe pspgne scores to a range that can be set on the command linewith the default range [0. What fraction of all instances of a w -wide subsequence or w -mer across both sequence sets occur in the primary set?
The MEME Suite
Use for educational, research and non-profit purposes is permitted. Choose the width with the biggest maximum score before scaling.
On a real machine iMac, 3.
For DNA, you also have the option to score matches on both strands: The maximum width is set to