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Insertion and deletion of words: Determinism and reversibility [chapter]

Lila Kari
1992 Lecture Notes in Computer Science  
Necessary and sufficient conditions, under which the result of sequential insertion or deletion of two words is a singleton set, are given.  ...  They are connected with the operations of sequential insertion and deletion, which are nondeterministic versions of catenation and right/ left quotient.  ...  The operations of sequential insertion and sequential deletion (called in the sequel, shortly, insertion and deletion), defined and studied in [2] play an important role in understanding the mechanisms  ... 
doi:10.1007/3-540-55808-x_30 fatcat:qftpxik5ebfgboxuteeoifniem


2011 International Journal of Foundations of Computer Science  
A general framework of parallel insertion and deletion based on p-schemata is proposed. A p-schema is a set of tuples of words.  ...  When being used for parallel insertion of a language into a word, an element of p-schema specifies how to split the word into factors between which the language to be inserted.  ...  This research was supported by Natural Sciences and Engineering Research Council of Canada Discovery Grant R2824A01, and Canada Research Chair Award to L. K.  ... 
doi:10.1142/s0129054111008945 fatcat:4hgm67sun5hr7j7skq3j2pb3yu

Pattern recognition of strings with substitutions, insertions, deletions and generalized transpositions

B.J. Oommen, R.K.S. Loke
1997 Pattern Recognition  
The traditional case which has been extensively studied in the literature is the one in which Y contains substitution, insertion and deletion (SID) errors.  ...  The paper includes experimental results involving sub-dictionaries of the most common English words which demonstrate the superiority of our system over existing methods.  ...  Latika Khanna of the School of Computer Science at Carleton for her assistance in proofreading the manuscript.  ... 
doi:10.1016/s0031-3203(96)00101-x fatcat:ptgtaxjoube2xcw2yegumqt5ze

Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes

M. S. Taylor
2004 Genome Research  
Overall, we found an excess of deletions over insertions, particularly for the rat lineage (70% excess). Sequence slippage accounts for at least 52% of insertions and 38% of deletions.  ...  There is a specific enrichment of CpG dinucleotides in close proximity to insertion events, and both insertions and deletions are more common in higher G+C content sequences.  ...  M.S.T. and R.R.C. are supported by the Wellcome Trust and C.P.P. by the UK Medical Research Council. The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.1977804 pmid:15059996 pmcid:PMC383299 fatcat:uxma372gwrfrpf5accjh7zpyg4

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes

Z. Zhang
2003 Nucleic Acids Research  
Nucleotide substitution, insertion and deletion (indel) events are the major driving forces that have shaped genomes.  ...  However, unexpectedly, the frequency of 3 bp deletions (in contrast to 3 bp insertions) violates this trend, being considerably higher than that of 2 bp deletions.  ...  ACKNOWLEDGEMENTS Z.Z. thanks Paul Harrison for scintillating discussions and Duncan Milburn, Yin Liu and Nat Echols for computational assistance.  ... 
doi:10.1093/nar/gkg745 pmid:12954770 pmcid:PMC203328 fatcat:4peybwjfwbhongr2m2ue2wg2o4

Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms

J.R. Pimenta, S.D.J. Pena
2010 Genetics and Molecular Research  
Thus, especially because of its simplicity and low cost, and the fact that it is composed of genomic markers that have very low mutation rates, it represents a useful new tool for human paternity testing  ...  The average heterozygosity (gene diversity) per locus was 0.48, and the combined probability of identity (matching probability) for the 40-locus set was 3.48 x 10 -17 .  ...  ACKNOWLEDGMENTS Research supported by CNPq of Brazil. J.R. Pimenta was the recipient of a fellowship from the Rhae Program of CNPq.  ... 
doi:10.4238/vol9-1gmr838 pmid:20391344 fatcat:4ohffkjl3vhqrfjf75arfnl6du

Multiple homoplasious insertions and deletions of a Triticeae (Poaceae) DNA transposon: a phylogenetic perspective

Roberta J Mason-Gamer
2007 BMC Evolutionary Biology  
Conclusion: Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a Stowaway-like element has undergone multiple deletions from and insertions into  ...  The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing Stowaway activity has never been observed  ...  Acknowledgements Thanks to members of the Wichman Lab transposable element journal club (Holly Wichman, LuAnn Scott, Mac Cantrell, and Issac Erickson) and to Brandon Gaut for valuable comments on an earlier  ... 
doi:10.1186/1471-2148-7-92 pmid:17570855 pmcid:PMC1925063 fatcat:meo3soyplvg5vkg45opdrmsqlu

Linear Time Additively Exact Algorithm for Transformation of Chain-Cycle Graphs for Arbitrary Costs of Deletions and Insertions

Konstantin Gorbunov, Vassily Lyubetsky
2020 Mathematics  
We assume that the double cut and join operations have identical costs, and costs of the deletion and insertion operations are arbitrary strictly positive rational numbers.  ...  We propose a novel linear time algorithm which, given any directed weighted graphs a and b with vertex degrees 1 or 2, constructs a sequence of operations transforming a into b.  ...  Acknowledgments: We are grateful to the anonymous reviewers for their thorough review, and we highly appreciate the comments and suggestions, which significantly contributed to improving the quality of  ... 
doi:10.3390/math8112001 fatcat:5zdo5di3tbgatnp3qlozvg3krq

RNA-Editing with Combined Insertion and Deletion Preserves Regularity

Erik De Vink, Hans Zantema, Dragan Bosnacki
2013 Scientific Annals of Computer Science  
The formalism here allows for simultaneous insertion and deletion of string elements.  ...  We consider two elementary forms of string rewriting called guided insertion/deletion and guided rewriting.  ...  Acknowledgements We acknowledge fruitful feedback from Peter van der Gulik and detailed comment from the reviewers.  ... 
doi:10.7561/sacs.2013.1.39 fatcat:tbjfvn4eofepfb6drg77aihc5m

On the embedding capacity of DNA strands under substitution, insertion, and deletion mutations

Félix Balado, Nasir D. Memon, Jana Dittmann, Adnan M. Alattar, Edward J. Delp III
2010 Media Forensics and Security II  
On the embedding capacity of DNA strands under substitution, insertion, and deletion mutations Felix Balado, Proc. SPIE 7541, 754114 (2010).  ...  This is the main topic studied in this paper, where we consider that DNA sequences may be subject to substitution, insertion, and deletion mutations.  ...  We will consider herein three important types of mutations: substitutions, insertions and deletions.  ... 
doi:10.1117/12.838537 dblp:conf/mediaforensics/Balado10 fatcat:2rtupx6pxra5pokxcckefqjvey

Correlated Occurrence and Bypass of Frame-Shifting Insertion-Deletions (InDels) to Give Functional Proteins

Liat Rockah-Shmuel, Ágnes Tóth-Petróczy, Asaf Sela, Omri Wurtzel, Rotem Sorek, Dan S. Tawfik, Siv Gun Elisabet Andersson
2013 PLoS Genetics  
Short insertions and deletions (InDels) comprise an important part of the natural mutational repertoire. InDels are, however, highly deleterious, primarily because two-thirds result in frame-shifts.  ...  Besides an expected 8A repeat, other types of repeats, including short ones, and G and C repeats, were bypassed.  ...  Summary Homonucleotide repeats are exceptionally prone to insertions and/or deletions of bases (InDels).  ... 
doi:10.1371/journal.pgen.1003882 pmid:24204297 pmcid:PMC3812077 fatcat:25nretm7drector5s5ayrmbfle

List decoding subspace codes from insertions and deletions

Venkatesan Guruswami, Srivatsan Narayanan, Carol Wang
2012 Proceedings of the 3rd Innovations in Theoretical Computer Science Conference on - ITCS '12  
We present a construction of subspace codes along with an efficient algorithm for list decoding from both insertions and deletions, handling an information-theoretically maximum fraction of these with  ...  Ours is the first list decoding algorithm for subspace codes that can handle deletions; even one deletion can totally distort the structure of the basis of a subspace and is thus challenging to handle.  ...  (The ratios t/ℓ and r/ℓ are the fraction of insertions and deletions, respectively.) Proof.  ... 
doi:10.1145/2090236.2090252 dblp:conf/innovations/GuruswamiNW12 fatcat:jntjs2l5s5aefoolcvyolol2ea

Identification and Characterization of a Cryptic Genomic Deletion-Insertion in EYA1 Associated with Branchio-Otic Syndrome

Hao Zheng, Jun Xu, Yu Wang, Yun Lin, Qingqiang Hu, Xing Li, Jiusheng Chu, Changling Sun, Yongchuan Chai, Xiuhong Pang, Geng lin Li
2021 Neural Plasticity  
Sanger sequencing of this PCR product revealed that it is in fact a GRCh38/hg38:chr8:g.71318554_71374171delinsTGCC genomic deletion-insertion.  ...  Real-time PCR at multiple regions of EYA1 confirmed the existence of this genomic deletion and extended its 5 ′ boundary beyond the 5 ′ -UTR.  ...  The Government of China is also acknowledged for providing research grant.  ... 
doi:10.1155/2021/5524381 pmid:33880118 pmcid:PMC8046558 fatcat:3kop7awaonavlgzn6ymv6d5634

Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations [article]

Kiyoshi Ezawa, Dan Graur, Giddy Landan
2015 bioRxiv   pre-print
via insertions and deletions along time axis.  ...  BackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary  ...  In other words, F (x, δ ′ ω [l]) inserts δ ′ ω [l] between the x th and (x +1) th residues of ω ∈ Ω L( s ) .  ... 
doi:10.1101/023622 fatcat:omnq5uz7ubfwnacqrlszyisali

Deletion and duplication of the adenomatous polyposis coli gene resulting from an interchromosomal insertion involving 5(q22q23.3) in the father

2000 Journal of Medical Genetics  
The authors would like to thank Simon Roth who referred the proband to the Cytogenetics Department and Helwyn Morgan for referring subsequent prenatal samples.  ...  Interchromosomal insertions are individually rare events and in this family both a deletion and duplication of the inserted region were viable.  ...  In other words, alleles of genes whose products interfere with the determination, migration, or diVerentiation of ganglion cells of the enteric plexuses might, in the presence of a perturbed Ras signalling  ... 
doi:10.1136/jmg.37.2.141 pmid:10712105 pmcid:PMC1734530 fatcat:3uxp4up72rdsjfsfn7uoea2dwy
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