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Topic: Pseudocount

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	Informed Priors (Site not responding. Last check: 2007-09-09)
		Background pseudocounts are calculated as a percentage of the background observed counts.
		The pseudocount for a particular nucleotide for the ith position of a motif is then the value of the particular column in the ith row divided by 100 and multiplied by the estimated number of motif sites and the pseudocount weight.
		In this case, the pseudocount for a particular nucleotide for the ith position of a motif is then the value of the column in the ith row multiplied by the pseudocount weight.
	bayesweb.wadsworth.org /gibbs/prior.html (717 words)

	mhmms
		This is done by combining pseudocount probabilities derived from a score matrix (see the '--pam' and '--score-file' options below) with the emission frequencies.
		The weight on the pseudocount probabilities can be adjusted to any value greater than or equal to zero using the '--pseudo-weight' switch.
		The smaller the weight, the less effect the pseudocount probabilities have, and the closer the adjusted probabilities will be to the emission probabilities in the model.
	metameme.sdsc.edu /doc/mhmms.html (2151 words)

	Erpin Web Server Tutorial
		Pseudocounts introduce some articifical base or base-pair counts in the weigth matrix, that simulate what could have been observed in a larger sequence alignment.
		Use the -pcw parameter to set the pseudocount weight: at pcw=0 no pseudocount is used, and at pcw=1, profiles are 100% pseudocounts.
		In the absence of pseudocounts, the lod-scores of bases or basepairs that are never observed at a given position are set at the default arbitrary value of -20.
	tagc.univ-mrs.fr /erpin/doc.4.2.2.html (2431 words)

	Pseudocounts, just in case (Site not responding. Last check: 2007-09-09)
		No A is observed in the first position, but if we set P(A) = 0, then we ìrule outî a motif with A in the first position.
		This is especially important in the initial guesses, so that the true motif is not missed.
		Pseudocounts may be decreased or removed (e=0) in later stages.
	www.bioinfo.rpi.edu /~bystrc/courses/2003biol4540/lecture23/tsld018.htm (65 words)

	[No title]
		No pseudocount is added during and after the training process.
		It is a little surprising to see that this model and final.model are almost identical, except a 10^-6 difference on the transition vector of the seventh state, despite the fact that we started from a model in which skipping gap is allowed.
		PseudoCount is added during each iteration of EM (background to gap states, and normalized hydrophobic background to critical states).
	www.research.rutgers.edu /~paihuang/models.html (1227 words)

	Erpin documentation page
		Because of the limited size of some training sets, it is desirable to introduce some flexibility in profiles so that ERPIN can detect sequences with several mutations relative to training set sequences.
		The pseudocount substitution matrix is based on substitutions observed in a 16S rRNA alignments.
		A new parameter -pcw is used to set the level of pseudocounts introduced into profiles (pcw=0: no pseudocount; pcw=1:only pseudocounts; pcw=0.1: default).
	tagc.univ-mrs.fr /erpin/documentation.html (664 words)

	Bayesian interpretation of pseudocount regularizers (Site not responding. Last check: 2007-09-09)
		To apply these methods we have to view amino acids as being generated by a two-stage random process.
		This rather involved computation finally ends up with the pseudocount method for estimating the probability of an amino acid given a sample of amino acids.
		Previous work with pseudocounts has relied heavily on this Bayesian interpretation of the parameters, going so far as to assign
	cse.ucsc.edu /research/compbio/html_format_papers/tr-95-11/node30.html (568 words)

	motifBS
		Pseudocounts, as the name implies, are observations that go into our frequency table, that we did not actually observe.
		Also, this small pseudocount will be drowned out more and more as we add more data.
		As you might have guessed, determining a proper pseudocount is naturally a Bayesian problem and has been approached in that way.
	compbio.berkeley.edu /people/ed/motifBS.html (1554 words)

	[No title]
		INPUT FILES =========== There are two input files: one contains the sequences to be analyzed and one the information on the dictionary structure and pseudocounts for the Dirichlet prior probabilities.
		Each word is described first by a line indicating the name and length of the world, as well as the pseudocounts needed for the prior probability of the apparence of the word.
		This parameter is introduced so that prior strength can be controlled and modified, without need of modifying the input file, that can be based on counts observed in databases and becomes important, then, only for relative counts.
	www.genetics.ucla.edu /software/vocabulon-README.txt (806 words)

	HMMTOP
		The option name, the equal sign and its value have to be written in one word (for example -sf=pir is accepted, but -sf= pir, -sf =pir or -sf = pir is not interpreted).
		The program uses a pseudocount vector whose data are in pseudo.dat file.
		FILES pseudo.dat Data for calculating pseudocount vector used by the optimization.
	www.enzim.hu /hmmtop1.1/doc/manual.html (792 words)

	GENOME 373: Genomic Informatics (Site not responding. Last check: 2007-09-09)
		The program should read from the command line a pseudocount weight parameter (which I called "beta" in class) and three file names.
		Add to each PSSM entry the product of the given pseudocount weight times the corresponding background frequency.
		Read the pseudocount weight and filenames from the command line (2 points).
	noble.gs.washington.edu /~noble/gs373/homework/hw4/hw4.html (503 words)

	[No title] (Site not responding. Last check: 2007-09-09)
		Now observe a number of events, reporting each and updating !
		write (, ) ' ' write (, ) ' 50 #18' write (, ) ' ' aacnts(1:acid_num) = 0 aacnts(18) = 50 call getwgt (aacnts, pseudocount) call rvec_print (acid_num, pseudocount, 'Pseudocounts:') !
		write (, ) ' ' write (, ) ' 49 #20' write (, ) ' ' aacnts(1:acid_num) = 0 aacnts(20) = 49 call getwgt (aacnts, pseudocount) call rvec_print (acid_num, pseudocount, 'Pseudocounts:') write (, ) ' ' write (, ) 'GETWGT_PRB' write (, ) ' Normal end of GETWGT tests.' stop end
	orion.math.iastate.edu /burkardt/b_src/getwgt/getwgt_prb.f90 (359 words)

	profiler man page
		It is possible to omit whitespace between a command line option and its parameter.
		This allows to give more or less importance to the data-dependent pseudocount values when calculating the PSI-Blast pseudo-frequencies (see equation [2] in Schaffer et al., 2001).
		This is a positive integer value weighting the data-dependent pseudocounts in equation [2] in Schaffer et al., 2001.
	www.isrec.isb-sib.ch /~vflegel/profiler/profiler_man.html (1611 words)

	Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements ...
		Sensitivity curves showing the benefits of restricted score rescaling and of tuning the pseudocount parameter and the purging percentage.
		observations for that column, and ß is the pseudocount
		Thus it may be advisable to choose the pseudocount parameter
	nar.oxfordjournals.org /cgi/content/full/29/14/2994 (6286 words)

	Homologous search help (Site not responding. Last check: 2007-09-09)
		There is the set of parameters for profile calculating(if use multiply alignment as a query).
		use square root estimation for the pseudocount parameter
		There is the set of parameters for alignment algorithm, which control alignment processing.
	strand.imb.ac.ru /saadi/hsearch_help.htm (263 words)

	[No title] (Site not responding. Last check: 2007-09-09)
		Estimate the emission parameters using the Add-one Pseudocount method given the background vector EMBED Equation.3 .
		Hit the Background Pseudocount field to enable background pseudocount parameter estimation.
		Try changing the emission pseudocount constant A to a large number, like e.g.
	xray.bmc.uu.se /~patrik/bioinf/hmm/HMMlab_X3_2006_fix.doc (2456 words)

	about Digree of conservation/variability at each alignment site (Site not responding. Last check: 2007-09-09)
		Select the method of ouputting the result from among "Numeriical Table", "Line Plot" and "PDB File".
		If pseudocount is introduced, select "execute" from the pulldown menu below.
		If pseudocount is introduced, select "execute" from the pulldown menu.This option is not displayed at "Valder and Thornton(with score table)" and "Sander and Schneider(with score table)".
	timpani.genome.ad.jp /~ash/digree_ex.html (482 words)

	PFM documentation.
		Args : -small_sample_correction # undef (default), 'schneider' or 'pseudocounts'
		and B an arbitrary pseudocount value or expression (for no pseudocounts
		For a given position i, the deviation from random distribution in bits
	forkhead.cgb.ki.se /TFBS/DOC/TFBS/Matrix/PFM.html (695 words)

	[No title] (Site not responding. Last check: 2007-09-09)
		my $pseudocount = 0.1; my $uniform_background = 0.25; my @characters = ("A", "C", "G", "T"); # Parse the command line.
		for (my $position = 0; $position < $seq_length; $position++) { my $character = uc(substr($line, $position, 1)); $counts{$position, $character}++; } $num_seqs++; } close(SEQUENCE_FILE); print(STDERR "Read $num_seqs sequences of length $seq_length.\n"); # Add pseudocounts, and keep track of column sums.
		my @column_sums; foreach my $character (@characters) { for (my $position = 0; $position < $seq_length; $position++) { $counts{$position, $character} += $pseudocount; $column_sums[$position] += $counts{$position, $character}; } } # Divide through to get frequencies.
	www.gs.washington.edu /~noble/gs559/homework/compute-pssm.pl (252 words)

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