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To: js1138
In order to make even a wild guess about the probability of this being adventitious, you would need to draw up a table of segment lengths of conserved code and see if the lengths can be placed in a normal distribution.

That has been done. Have you ever used BLAST?

PSI-BLAST is an iterative program to search a database for proteins with distant similarity to a query sequence. We investigated over a dozen modifications to the methods used in PSI-BLAST, with the goal of improving accuracy in finding true positive matches. To evaluate performance we used a set of 103 queries for which the true positives in yeast had been annotated by human experts, and a popular measure of retrieval accuracy (ROC) that can be normalized to take on values between 0 (worst) and 1 (best). The modifications we consider novel improve the ROC score from 0.758 +/- 0.005 to 0.895 +/- 0.003. This does not include the benefits from four modifications we included in the 'baseline' version, even though they were not implemented in PSI-BLAST version 2.0. The improvement in accuracy was confirmed on a small second test set. This test involved analyzing three protein families with curated lists of true positives from the non-redundant protein database. The modification that accounts for the majority of the improvement is the use, for each database sequence, of a position-specific scoring system tuned to that sequence's amino acid composition. The use of composition-based statistics is particularly beneficial for large-scale automated applications of PSI-BLAST.

146 posted on 06/08/2004 12:42:53 PM PDT by AndrewC (I am a Bertrand Russell agnostic, even an atheist.</sarcasm>)
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To: AndrewC

Could you translate that into English and show me where to find the spread of conserved code lengths in simple chart form?


147 posted on 06/08/2004 12:47:52 PM PDT by js1138 (In a minute there is time, for decisions and revisions which a minute will reverse. J Forbes Kerry)
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