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http://blast.ncbi.nlm.nih.gov/Blast.cgi

In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? The question mark says it means that:

Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.

Another parameter is there called pseudocount. Did not understand that too. Could not understand what this means, someone please explain in simple language.

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PSI-BLAST is an iterative algorithm. Each cycle it uses a model (the position-specific scoring matrix, or PSSM) to search for sequences matching the model, next updates the model with the sequences found, and then runs the search again with the updated model. That P-value controls which of the sequences found in each iteration should be included in the new model (i.e. only include those sequences satisfying the P-value).

Regarding the pseudocounts, this is a value to be added to each column in the PSSM. The reason is to avoid zero count entries, which may give problems later. But as the help suggests:

Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented.

It is probably OK to leave the default option unless you have some reason to change it.

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