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Identification of Short Motifs for Comparing Biological Sequences
Identification of Short Motifs for Comparing Biological Sequences

Absolute o(logm) error in approximating random set covering: an
Absolute o(logm) error in approximating random set covering: an

Kernels for gene regulatory regions
Kernels for gene regulatory regions

Abstract - BioMed Central
Abstract - BioMed Central

Guide for Bioinformatics Project Module 3 - SGD-Wiki
Guide for Bioinformatics Project Module 3 - SGD-Wiki

... what   may   be   the   most   important   residues   in   this   domain   based   on   those   that   have   been   unchanged   throughout   evolution.  To  do  this  HMM  Logos  provide  the  researcher  with  a  quick  overview  of   ...
Greedy Closure Evolutionary Algorithms
Greedy Closure Evolutionary Algorithms

PPTX - Tandy Warnow
PPTX - Tandy Warnow

... • MetaPhyler, MetaPhlAn, and mOTU are marker-based techniques (but use different marker genes). ...
A Genetic Algorithm Approach to Solve for Multiple Solutions of
A Genetic Algorithm Approach to Solve for Multiple Solutions of

... A Genetic Algorithm, through Selection, Cross-over and Mutation operations, finds the individuals that have the best fitness values and combines them to produce individuals that offer better fitness values than their parents. This process continues until the population converges around the single indiv ...
doc
doc

File - Bengt Hansson
File - Bengt Hansson

HJ2614551459
HJ2614551459

MacVector 14.0 Getting Started Guide
MacVector 14.0 Getting Started Guide

Quantile Regression for Large-scale Applications
Quantile Regression for Large-scale Applications

... ates (Koenker & Bassett, 1978), in a manner analogous to the way in which Least-squares regression estimates the conditional mean. The Least Absolute Deviations regression (i.e., `1 regression) is a special case of quantile regression that involves computing the median of the conditional distributio ...
what is alignment? - UWI St. Augustine
what is alignment? - UWI St. Augustine

... Significance of local sequence alignment •In global alignment, an attempt is made to align the entire sequences, as many characters as possible. • In local alignment, stretches of sequence with the highest density of matches are given the highest priority, •generating one or more islands of matches ...
Halpotyping - CS, Technion
Halpotyping - CS, Technion

... In this discussion was presented a new method, Gibbs-Jump, for haplotype analysis, which explores the whole distribution of haplotypes conditional on the observed phenotypes.  The method is very time-efficient.  The result accuracy was compared to obtained by other methods (described by Sobol).  ...
Lecture 3 — October 16th 3.1 K-means
Lecture 3 — October 16th 3.1 K-means

Eiben Chapter2
Eiben Chapter2

Construction of PANM Database (Protostome DB) for rapid
Construction of PANM Database (Protostome DB) for rapid

... A stand-alone BLAST server is available that provides a convenient and amenable platform for the analysis of molluscan sequence information especially the EST sequences generated by traditional sequencing methods. However, it is found that the server has limitations in the annotation of molluscan se ...
Nucleotide sequence analysis - Bioinformatics Unit
Nucleotide sequence analysis - Bioinformatics Unit

1 Divide and Conquer with Reduce
1 Divide and Conquer with Reduce

... to believe that any such algorithms will have to keep a cumulative “sum,” computing each output value by relying on the “sum” of the all values before it. In this lecture, we’ll see a technique that allow us to implement scan in parallel. Let’s talk about another algorithmic technique: contraction. ...
from Terrel Smith`s class, MS-Powerpoint slide set
from Terrel Smith`s class, MS-Powerpoint slide set

... – A statement of this form is very useful in proving that algorithms terminate in a finite number of steps • If a given set is in decreasing order, meaning , and for all i, i ≥ 1, the sequence is finite because the well-ordering principle states that the set has a least element . This set can repres ...
Filtering Actions of Few Probabilistic Effects
Filtering Actions of Few Probabilistic Effects

IOSR Journal of Computer Engineering (IOSR-JCE)
IOSR Journal of Computer Engineering (IOSR-JCE)

... a kind of heuristic random search algorithm based on group difference and the optimization is finished using real encoding in continuous space. But it is incapable of “survival of the fittest” during the selection process. The mutation operation in the algorithm only aims at the newly generated indi ...
Coarse-Grained ParallelGeneticAlgorithm to solve the Shortest Path
Coarse-Grained ParallelGeneticAlgorithm to solve the Shortest Path

algo and flow chart
algo and flow chart

< 1 ... 3 4 5 6 7 8 9 10 11 ... 21 >

Smith–Waterman algorithm

The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings or nucleotide or protein sequences. Instead of looking at the total sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.The algorithm was first proposed by Temple F. Smith and Michael S. Waterman in 1981. Like the Needleman–Wunsch algorithm, of which it is a variation, Smith–Waterman is a dynamic programming algorithm. As such, it has the desirable property that it is guaranteed to find the optimal local alignment with respect to the scoring system being used (which includes the substitution matrix and the gap-scoring scheme). The main difference to the Needleman–Wunsch algorithm is that negative scoring matrix cells are set to zero, which renders the (thus positively scoring) local alignments visible. Backtracking starts at the highest scoring matrix cell and proceeds until a cell with score zero is encountered, yielding the highest scoring local alignment. One does not actually implement the algorithm as described because improved alternatives are now available that have better scaling (Gotoh, 1982) and are more accurate (Altschul and Erickson, 1986).
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