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'''MaMF''', or Mammalian Motif Finder, is an algorithm for identifying [[Sequence motif|motifs]] to which [[transcription factors]] bind.<ref>{{cite journal ...res an [[n-mer]], and each sequence forms an ungapped [[Sequence alignment|alignment]] with a substring of length w from the string of length 2w around the matc ...

...and occur only once in each genome are almost certainly part of the global alignment. ...orithms in Bioinformatics">{{cite book |last1=Wing-Kin |first1=Sung |title=Algorithms in Bioinformatics: A Practical Introduction |date=2010 |publisher=Chapman & ...

...be either of [[genomic]], "[[transcriptome|transcriptomic]]" ([[expressed sequence tag|ESTs]]) or [[protein]] origin. ...o group sequences originating from the same [[gene]] before the ESTs are [[sequence assembly|assembled]] to reconstruct the original [[mRNA]]. ...

...tree is minimized. Tree alignment can be accomplished using one of several algorithms with various trade-offs between manageable tree size and computational effo ...last1=Elias | first1=Isaac | title=Settling the intractability of multiple alignment | doi=10.1089/cmb.2006.13.1323 | year=2006 | journal=J Comput Biol | volume ...

...10.1145/1824795.1824798 | title = A taxonomy of sequential pattern mining algorithms | journal = ACM Computing Surveys | volume = 43 | pages = 1–41 | year = 201 ...which is typically based on [[String (computer science)|string processing algorithms]] and ''itemset mining'' which is typically based on [[association rule le ...

{{Short description|DNA and protein sequence alignment software package}} '''FASTA''' is a [[DNA]] and [[protein]] [[sequence alignment]] software package first described by [[David J. Lipman]] and [[William Pea ...

| thesis_title = Aspects of Biological Sequence Comparison | title = Basic Local Alignment Search Tool ...

...cause an alignment to become meaningless. Gap penalties are used to adjust alignment scores based on the number and length of gaps. The five main types of gap p ...ce alignments, gaps are represented as dashes(-) on a protein/DNA sequence alignment.<ref name="rosalind_glossary" /> ...

...achi|first2=I.|last3=Nakamura|first3=Y.|title=The International Nucleotide Sequence Database Collaboration|journal=Nucleic Acids Research|date=23 November 2010 ...the sequence database.<ref>{{cite book |last1=Sung |first1=Wing-Kin |title=Algorithms in bioinformatics : a practical introduction |date=2010 |publisher=Chapman ...

...ip between the structures deposited in the PDB and the [[Primary structure|sequence]] of the protein which one wishes to model. ...te is selected, the structural model of the sequence is built based on the alignment with the chosen template. Protein threading is based on two basic observati ...

...signment problem|quadratic assignment]], [[Sequence alignment|DNA sequence alignment]], [[Maxcut|max-cut]] and buffer allocation problems. * [[Genetic algorithms]] ...

...52 | pmc = 168907 | doi = 10.1093/nar/gkg500 }}</ref> The software and its algorithms have gone through several iterations, with '''ClustalΩ (Omega)''' being the [[File:Multiple_Sequence_Alignment_Using_ClustalW.jpg|thumb|Multiple sequence alignment of [[Cyclin-dependent kinase 4|CDK4 protein]] generated with ClustalW. Arro ...

...l,d)-Motif Problem with Negative Set]", Proceedings of the 5th Workshop on Algorithms in Bioinformatics (WABI 2005), (October 2005) (accepted) ...and Henry C.M. Leung, "[http://www.cs.hku.hk/~chin/paper/apbc05.pdf Voting Algorithms for Discovering Long Motifs]", Proceedings of the Third Asia-Pacific Bioinf ...

|class= [[Sequence alignment]] |image= Needleman-Wunsch pairwise sequence alignment.png ...

...i.e., experimental data obtained with technologies that require the genome sequence, such as genomic [[DNA microarrays]]). These, in combination with computati ...k |last=Mount |first=David | name-list-style = vanc |title=Bioinformatics, Sequence and Genome Analysis |publisher=Cold Spring Harbor Laboratory Press |year=20 ...

...helped to design the proteins along with [[protein structure prediction]] algorithms.<ref name="Kuhlman-2003" /> The resulting sequence of residues is: ...

...nt (especially with "dumb" DP) and more weight on how to get distance from alignment|date=December 2023}} ...[[structural alignment|structural]] and [[sequence alignment|sequential]] alignment, and for the determination of protein structures from [[Nuclear magnetic re ...

{{Short description|Method of DNA sequence reconstruction}} ...enomic]] DNA, or [[Transcription (genetics)|gene transcript]] ([[expressed sequence tag|ESTs]]).<ref name="Sohn_2018" /> ...

...ifference between the two algorithms consists in that the ''optimal string alignment algorithm'' computes the number of edit operations needed to make the strin ...''CA''' → '''A''' → '''AB''' → '''ABC'''. Note that for the optimal string alignment distance, the [[triangle inequality]] does not hold: OSA('''CA''',&nbsp;''' ...

...vid |year=1996 |chapter=The Lack of A Priori Distinctions between Learning Algorithms |title=Neural Computation |volume=8 |issue=7 |pages=1341–1390 |doi=10.1162/ ...n this context is a particular [[objective function]], and a result is a [[sequence]] of values obtained in evaluation of [[candidate solutions]] in the [[func ...