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	Gap penalty - Wikipedia, the free encyclopedia
		Gap penalties contribute to the overall score of alignments, and therefore, the size of the gap penalty relative to the entries in the similarity matrix affects the alignment that is finally selected.
		Under a linear gap penalty, the overall penalty for one large gap is the same as for many small gaps.
		Therefore, affine gap penalties have a gap opening penalty, c, and a gap extension penalty, e.
	en.wikipedia.org /wiki/Gap_penalty (251 words)

	BioinformaticsOnline.org
		By subtracting any remaining end gap penalties from all positions in the last column and bottom row (not shown), one finds that the best score is actually -5 in the right-hand, lowest corner of the matrix obtained by a diagonal move to this position, giving a score of -8+3 = -5.
		Another method of testing a scoring matrix and gap penalty combination is to perform a search of a sequence database with a known member of a protein family and to find how many members of the family are found when the same matrix/penalty is used.
		The gap penalty scores found to be useful for the BLOSUM50 matrix (-13 to open the gap and -1 for each additional position) are also in the useful range for obtaining local alignments by the Smith-Waterman algorithm (Altschul and Gish 1996).
	www.bioinformaticsonline.org /ch/ch03/supp-all.html (12825 words)

	Jordan Nash's Bioinformatics Page (Site not responding. Last check: 2007-11-03)
		When a gap penalty is put into effect, the similarity went down for my two DNA sequences Ski and SnoN.
		However the gap penalty did not affect the similarity of the two protein sequences because they were almost identical anyway.
		This is not surprising that a gap penalty would not yield a different result as the only mismatches that would take place would be when the shorter sequence terminated.
	webpages.marshall.edu /~nash10/assignment4.html (527 words)

	Week 3 - Approximate String Alignment continued
		Gaps in a sequence alignment, caused by insertions/deletions, are sequences of spaces in a single string.
		A gap of more than one space can be created by one mutational event and so in a more plausible model the spaces in a gap are not treated as separate events.
		Because the gap penalty increases in a constant amount after the first gap, we dont have to know how long the gap is, just whether or not we are opening a new gap or if we are adding to an already established gap.
	www.inf.ethz.ch /personal/cgina/courses/compbio/week3/week3/week3.html (632 words)

	[No title]
		Gap penalties -11-3, -16-1, -18-1, and -19-1 gave high sensitivity, but we chose -11-3 as the best working gap penalty because the different in sensitivity is insignificant and because -16-1, -18-1 and -19-1 are seldom in the list of gap penalty choice in BLAST.
		Gap penalty -12-2 with BLOSUM50, -10-1 with BLOSUM62, and -11-3 with PAM250.
		Gap penalty –16-0 is an outstanding gap penalty value, the sensitivity value for FASTA, ktup2 is lower than for other gap penalties.
	www.sbc.su.se /~arne/xjobb/amin.html (6735 words)

	Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function -- ...
		Gaps that occur at the junction of a helix and a strand (g
		Probability distribution of gaps, by length, for the combined data (irrespective of secondary structure type), in (A) the SHoPP database and (B) the DAPS database (20).
		the breakpoint at the gap of length 3 (equation 2 and Fig.
	nar.oxfordjournals.org /cgi/content/full/32/9/2838 (3058 words)

	clustalw
		Gap characters "-" are used to indicate the positions of gaps in the multiple alignment.
		A gap penalty mask is a series of numbers between 1 and 9, one per position in the alignment.
		The format for gap penalty masks and secondary structure masks is explained in the help under option 0 (secondary structure options).
	www.bioinformatics.ubc.ca /resources/tools/index.php?name=clustalw (6176 words)

	Lab1
		Gap is an implementation of the Needleman-Wunsch algorithm.
		Two gaps have been inserted into the alignment to realize one match, the C-C. (the two one base gaps subtract 22 from the score and the match adds 10, this replaces what we've been seeing as two mismatches, which would subtract 18 from the score).
		Run bestfit and gap on the two amino acid sequences, aefur.pep and bpfur.pep using the default parameters.
	www.bimcore.emory.edu /home/Kins/IBS574/Lab1/Lab1.html (631 words)

	Help for secondary structure / gap penalty masks (Site not responding. Last check: 2007-11-03)
		The masks work by raising gap penalties in specified regions (typically secondary structure elements) so that gaps are preferentially opened in the less well conserved regions (typically surface loops).
		Basic gap penalties are multiplied by the amount specified.
		Either a structure or penalty mask or both may be used.
	www.sacs.ucsf.edu /Documentation/seqsoftware/ClustalW1.7/helpB.html (514 words)

	ALIGN2D -- align sequences with structures (Site not responding. Last check: 2007-11-03)
		It is the same as the ALIGN command except that a variable gap opening penalty is used.
		This gap penalty depends on the 3D structure of all sequences in block 1.
		The linear gap penalty function for inserting a gap in block 1 of structures is:
	bob.usuf2.usuhs.mil /bid510/modeller_manual/node97.html (492 words)

	Affine Gap Penalties
		The affine gap cost model penalizes insertions and deletions using a linear function in which one term is length independent, and the other is length dependent.
		Under their current scoring system, which uses a regular gap penalty, the alignment could also be written as in figure 2.
		For the first alignment this results in a new score of 4 (Figure 3) as now when a gap is extended (there is more than one _ in a row) the score is only -1, whereas previously each gap received a score of -2 whether it was a new gap or an extension.
	homepage.usask.ca /~ctl271/857/affine_gap_penalties.shtml (673 words)

	3D SIG ISMB Special Interest Scientific Registration List (Site not responding. Last check: 2007-11-03)
		The affine gap penalty scheme recognizes that it costs to open a gap as well as to extend an existing one, and has proved to be superior to length proportional gap costs, which often produce a large number of short insertions or deletions.
		The computational complexity for a bilinear gap penalty function has been shown to be O(mn), the same as for the affine gap penalty, indicating that computational cost would not be a factor in the implementation of such a function in homology detection algorithms.
		Though the logarithm of the probability distribution of gap lengths for all gap types exhibit the same bilinear behavior, the parameters describing the regression lines are clearly a function of the secondary structure of residues flanking the gap.
	www.weizmann.ac.il /usersfiles/3dsig/abstracts/2004/86.html (509 words)

	Help CLUSTAL W on the WEB
		Gap extension penalty: the penalty for extending a gap by 1 residue.
		The basic parameters to control this are two gap penalties and the scores for various identical/non-indentical residues.
		RESIDUE SPECIFIC PENALTIES are amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence.
	www.med.nyu.edu /rcr/rcr/clustalw-help.html (3813 words)

	..: institute for computational biomedicine :: help
		The parameters most likely to affect the quality of the alignment are the gap penalty (GapOpen), the gap-extension penalty (GapExt), and to a lesser extent, the substitution matrix.
		If the position of the gap is correctly identified, then the negative score incurred by the GapOpen penalty will be more than compensated for by enhanced positive scores further down the alignment.
		To take into account the fact that a point deletion is more or less as likely to occur as a longer deletion, the penalty to extend a gap is minimal, so that a gap of x residues is not penalised x times as much as a single residue deletion.
	icb.med.cornell.edu /education/courses/introtobio/h-clustalw.xml (1303 words)

	EMBOSS: water
		A penalty is subtracted from the score for each gap opened (the 'gap open' penalty) and a penalty is subtracted from the score for the total number of gap spaces multiplied by a cost (the 'gap extension' penalty).
		Typically, the cost of extending a gap is set to be 5-10 times lower than the cost for opening a gap.
		The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap.
	www.psc.edu /general/software/packages/emboss/water.html (1260 words)

	Methods
		Since a gap of more than space can be cuased by a single genetic mutation, the protein alignment model should consder the statistical distribution of gaps, in addition to the number of gaps in the alignment(6).
		The fixed gap penalty scheme is that a fixed value is selected as a gap penalty independent on the gap length.
		When a gap first happens, the opening gap penalty is applied and an extension penalty is applied to the score with contiguous gaps.
	www.ece.utexas.edu /~hjshin/Methods.htm (1322 words)

	[Bioperl-l] What is the gap penalty function for BLOSUM62?
		The most effective penalty for the first residue in a gap (q+r) changes as a function of evolutionary distance, while the gap extension penalty for additional residues (r) does not.
		Our results provide an empirical basis for selection of gap penalties and demonstrate how optimal gap penalties behave as a function of the target evolutionary distance of the substitution matrix.
		These gap penalties can improve expectation values by at least one order of magnitude when searching with short sequences, and improve the alignment of proteins containing short sequences repeated in tandem.
	www.bioperl.org /pipermail/bioperl-l/2003-July/012897.html (368 words)

	Assignment 4 (Site not responding. Last check: 2007-11-03)
		When using gap, the results given good similarity, when gap penalties were introduced it didn't change.
		The best fit at the default found numerous mismatches, but when the penalty was not assessed it let many more matches be made with less mismatches.
		The results from the GAP peptide are moved over to match the peptide sequence to the end of the longer sequence.
	webpages.marshall.edu /~spencer13/Assignment4.htm (335 words)

	Gap Penalty (Site not responding. Last check: 2007-11-03)
		Opening gap is a penalty for the initiation of the gap in sequence or in structure.
		This penalty is applied for encreasing already existing by one residue.
		As well as in the opening gap penalty case, increasing an extension gap penalty may increase the significance of the match.
	123d.ncifcrf.gov /gap.html (108 words)

	Needleman-Wunsch algorithm
		It is determined by "match award", "mismatch penalty" and "gap penalty".
		Also, there is an assumption behind: the row(-1st row) and column(-1st col) that are not shown in the matrix, but will be used to compute first row(0th row) and column(0th col) are all 0s, which means an empty string matched to a sequence in case of without gap penalty.
		If there is a down arrow, insert a gap for X sequence, a right arrow, insert a gap for Y sequence.
	www.cs.uh.edu /~zhenzhao/Review/alignment.htm (831 words)

	[No title] (Site not responding. Last check: 2007-11-03)
		So the actually gap penalty for position i = GapPen x M(i)/100, where M(i) is the gap penalty multiplier from the profile at position i and GapPen is the gap penalty entered in PROFILESEARCH.
		So, if the value of the multiplier is 100 (the usual situation) then the gap penalty at the position will be the gap penalty you enter in PROFILESEARCH.
		Since gaps appear to occur more frequently in coil regions, you might want to lower the multiplier for those areas.
	www.csb.yale.edu /userguides/datamanip/profile/profiler_3d.html (219 words)

	Clustalw
		Gap penalty masks is to be supplied with the input sequences.
		These are derived from the original table of relative frequencies of gaps adjacent to each residue (12) by subtraction from 2.0.
		Hydrophilic gap penalties are used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common.
	cbi.labri.fr /outils/Pise/clustalw.html (3015 words)

	Unix (Site not responding. Last check: 2007-11-03)
		To compensate for this, and to differentiate between cases like the one above, the gap penalty is made up of two factors:
		The gap creation penalty - subtracted from the alignment quality whenever a gap is opened.
		The gap extension penalty - subtracted from the alignment quality according to the length of the gap.
	www.biu.ac.il /LS/bio/Presentation/seqcom/seqcomp8.html (125 words)

	EMBOSS: matcher
		-gaplength integer The gap length, or gap extension, penalty is added to the standard gap penalty for each base or residue in the gap.
		The gap penalty is the score taken away when a gap is created.
		The gap length, or gap extension, penalty is added to the standard gap penalty for each base or residue in the gap.
	bioinformatics.biu.ac.il /EMBOSS/matcher.html (1920 words)

	EMBOSS: needle
		This program uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length.
		The Needleman-Wunsch algorithm is a member of the class of algorithms that can calculate the best score and alignment in the order of mn steps, (where 'n' and 'm' are the lengths of the two sequences).
		Needle finds an alignment with the maximum possible score where the score of an alignment is equal to the sum of the matches taken from the scoring matrix.
	homes.esat.kuleuven.be /~thijs/EMBOSS/needle.html (1240 words)

	EMMA (Site not responding. Last check: 2007-11-03)
		The penalty for opening a gap in the pairwise alignments.
		The penalty for extending a gap by 1 residue in the pairwise alignments.
		This is a penalty for each gap in the fast alignments.
	genopole.toulouse.inra.fr /bioinfo/emboss/emma.html (1588 words)

	Clustal W Help
		GAPS in the old alignments are indicated using the "-"
		A gap penalty mask is a series of numbers between 1 and 9, one per position in
		The format for gap penalty masks and secondary structure masks is explained
	www.fut.es /~rhd/personal/TEMA4/CLUSTALW.HTM (4110 words)

	EMBOSS: sigscan
		A signature is matched to a protein sequence and scored using a dynamic programming algorithm which permits variability in gap distance and residue type.
		-gape float The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap.
		Important - In the case where a signature file is generated by hand, it is essential that the gap data given is listed in order of increasing gap size.
	www.sacs.ucsf.edu /Documentation/emboss/sigscan.html (1556 words)

	EMBOSS: nrscope
		If a pair of proteins achieve greater than a threshold percentage sequence identity (specified by the user) the shortest sequence is discarded.
		The user must specify gap insertion and extension penalties and a residue substitution matrix for use in the alignments.
		The gap insertion penalty is the score taken away when a gap is created.
	www.biochem.uwo.ca /rt/man/html_emboss/nrscope.html (1186 words)

	EMBOSS: seqnr
		All further queries should go to Jon Ison.
		Mandatory qualifiers: [-path] string Directory of redundant database search results [-extn] string File extension of redundant database search results files [-outpath] string Directory for proccessed results [-outextn] string File extension for proccessed results files [-datafile] matrixf Residue substitution matrix [-gapopen] float The gap insertion penalty is the score taken away when a gap is created.
		The output is a standard EMBOSS report file.
	www.csc.fi /molbio/progs/emboss/Apps/seqnr.html (640 words)

	NEEDLE (Site not responding. Last check: 2007-11-03)
		OR you can type your data in the next area, or cut and paste it from another application.
		Default: 10.0 for any sequence Allowed values: Floating point number from 1.0 to 100.0
		Default: 0.5 for any sequence Allowed values: Floating point number from 0.0 to 10.0
	genopole.toulouse.inra.fr /bioinfo/emboss/needle.html (289 words)

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