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Anaplasma marginale major surface protein 3 is encoded by a polymorphic, multigene family

A R Alleman, G H Palmer, T C McGuire, T F McElwain, L E Perryman, A F Barbet
1997 Infection and Immunity  
Sequence analysis of three unique msp3 genes, msp3-12, msp3-11, and msp3-19, revealed both conserved and variant regions within the open reading frames.  ...  With msp3-12 as a probe, multiple, partially homologous gene copies were identified in the genomes of three A. marginale strains. These copies were widely distributed throughout the chromosome.  ...  open reading frame.  ... 
doi:10.1128/iai.65.1.156-163.1997 fatcat:mmxn5f4jh5f65bdhrw63b3wsci

FUSTr: a tool to find gene families under selection in transcriptomes

T. Jeffrey Cole, Michael S. Brewer
2018 PeerJ  
Single best Open Reading Frames from transcripts are then extracted using Transdecoder v3.0.1 (Haas et al., 2013) , providing .  ...  This typically entails homology searches in large amino acid sequence similarity networks with graph partitioning algorithms to cluster coding sequences into transitive groups (Andreev and Racke, 2006  ... 
doi:10.7717/peerj.4234 pmid:29372116 pmcid:PMC5775752 fatcat:2efzsqquvngdfprb4atahktuhu

FUSTr: a tool to find gene Families Under Selection in Transcriptomes [article]

Timothy Jeffrey Cole, Michael Scott Brewer
2017 bioRxiv   pre-print
Single best Open Reading Frames from transcripts are then extracted using Transdecoder v3.0.1 (Haas et al., 2013) , providing .  ...  This typically entails homology searches in large amino acid sequence similarity networks with graph partitioning algorithms to cluster coding sequences into transitive groups (Andreev and Racke, 2006  ... 
doi:10.1101/146951 fatcat:zocshaxnx5byjmdedp7lslimzi

Gene replacement by homologous recombination in plants [chapter]

Holger Puchta
2002 Functional Genomics  
After the elucidation of the sequence of the yeast genome a major effort was started to elucidate the biological function of all open reading frames of this organisms by targeted gene replacement via homologous  ...  The establishment of the complete sequence of the genome of Arabidopsis thaliana would principally allow a similar approach.  ...  With the complete sequence of the Arabidopsis genome at hand, multiple open reading frames with similarities to known genes of other organisms involted in repair and recombination can be identified (see  ... 
doi:10.1007/978-94-010-0448-0_12 fatcat:mypzh2xclbeexfxxxzosgj64xa

Highly efficient homology-driven genome editing in human T cells by combining zinc-finger nuclease mRNA and AAV6 donor delivery

Jianbin Wang, Joshua J. DeClercq, Samuel B. Hayward, Patrick Wai-Lun Li, David A. Shivak, Philip D. Gregory, Gary Lee, Michael C. Holmes
2015 Nucleic Acids Research  
Nucleasedriven genome editing provides a method in which to precisely target genetic changes to further enhance T cell function in vivo.  ...  We describe the development of a highly efficient method to genome edit both primary human CD8 and CD4 T cells by homology-directed repair at a pre-defined site of the genome.  ...  or transgene into a predetermined genomic target site.  ... 
doi:10.1093/nar/gkv1121 pmid:26527725 pmcid:PMC4756813 fatcat:wk6r4pgosrcopdlrwqwvxmnrke

Sequences enhancing cassava mosaic disease symptoms occur in the cassava genome and are associated with South African cassava mosaic virus infection

A. T. Maredza, F. Allie, G. Plata, M. E. C. Rey
2015 Molecular Genetics and Genomics  
The number of SEGS reads (normalised against total NGS sRNA reads) was quantified in T200 and TME3, modelled through a Poisson distribution, and lower and upper limits of confidence intervals calculated  ...  RNA from transcribed MITEs can regulate gene expression through RNA-directed gene methylation of adjacent genes (Buchmann et al. 2009) , and/or through Post Transcriptional Gene Silencing (PTGS) of homologous  ... 
doi:10.1007/s00438-015-1049-z pmid:25920485 fatcat:2d3scnqvjbhqzdz4naf76sq5vu

Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting Proteins [chapter]

Karen T. Girão, Fátima C. E. Oliveira, Kaio M. Farias, Italo M. C. Maia, Samara C. Silva, Carla R. F. Gadelha, Laura D. G. Carneiro, Ana C. L. Pacheco, Michel T. Kamimura, Michely C. Diniz, Maria C. Silva, Diana M. Oliveira
2008 Lecture Notes in Computer Science  
rule discovery and probabilistic relational models) with hidden Markov models (HMMs) and Viterbi algorithm (VA) to mine tetratricopeptide repeat (TPR), pentatricopeptide (PPR) and half-a-TPR (HAT) in genomes  ...  This TPR signature matrix was subsequently used to search for TPR motifs in the six reading frames of whole Leishmania genomes.  ...  Each TPR motif cluster was then investigated in detail by manually analyzing the positions and reading frames of the TPR motifs compared with available Leishmania genomes (1) open reading frame (ORF) models  ... 
doi:10.1007/978-3-540-88436-1_31 fatcat:72sozzbi3vajtdkpfsyoznilw4

Tracking genome engineering outcome at individual DNA breakpoints

Michael T Certo, Byoung Y Ryu, James E Annis, Mikhail Garibov, Jordan Jarjour, David J Rawlings, Andrew M Scharenberg
2011 Nature Methods  
Rare-cutting endonucleases, through their capacity to create a targeted DNA strand break, are one of the most promising of these technologies.  ...  Site-specific genome engineering technologies are increasingly important tools in the postgenomic era, where biotechnological objectives often require organisms with precisely modified genomes.  ...  We would like to thank Cherie Ramirez and Keith Jyoung for Zinc Finger Nucleases (Harvard University, Massachusetts General Hospital) and all members of the Northwest Genome Engineering Consortium (NGEC  ... 
doi:10.1038/nmeth.1648 pmid:21743461 pmcid:PMC3415300 fatcat:bg4h4imb2vbudjdp4uql3tsfxa

Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets

Kazuki Takabatake, Kazuki Izawa, Motohiro Akikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
2021 Genes  
In this paper, we propose a new, high-performance homology search algorithm that employs a two-step seed search strategy using multiple reduced amino acid alphabets to identify highly similar subsequences  ...  NCBI BLAST is the most widely used software for performing homology searches, but its speed is insufficient for the throughput of current DNA sequencers.  ...  (2) and Searching for Seeds (3) DNA sequence reads obtained by a DNA sequencer were translated into six frames and concatenated using the delimiter.  ... 
doi:10.3390/genes12091455 pmid:34573438 pmcid:PMC8469100 fatcat:neohyzn6bngpxdu53va3vm3rhy

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases

A. Wallqvist, Y. Fukunishi, L. R. Murphy, A. Fadel, R. M. Levy
2000 Bioinformatics  
Subsequently contributions from secondary structure are phased in and new homologous proteins are positively identified if their scores are consistent with the predetermined error rate.  ...  Incorporating predicted secondary structure information in the analysis of six small genomes yields an improvement in the homology detection of ∼20% over SSEARCH pairwise alignments, but no improvement  ...  For fold recognition in genomes, the open reading frames (ORF) from the following genomes were analyzed, Mycoplasma genitalium (MG) , Treponema pallidum (TP) (Fraser et al., 1998) , Methanococcus jannaschii  ... 
doi:10.1093/bioinformatics/16.11.988 pmid:11159310 fatcat:bmegjlrjonc5lho5khll2hfxga

Cloning, expression and localization of human BM88 shows that it maps to chromosome 11p15.5, a region implicated in Beckwith-Wiedemann syndrome and tumorigenesis

M Gaitanou, P Buanne, C Pappa, N Georgopoulou, A Mamalaki, F Tirone, R Matsas
2001 Biochemical Journal  
Porcine BM88 is a neuron-specific protein that enhances neuroblastoma cell differentiation in vitro and may be involved in neuronal differentiation in vivo.  ...  Here we report the identification, by Western blotting, of homologous proteins in human and mouse brain and the isolation of their respective cDNAs.  ...  By making use of our knowledge of porcine BM88 and searching through EST databases, we have now cloned and sequenced the homologous human and mouse BM88 cDNA molecules and we have investigated their expression  ... 
pmid:11311134 pmcid:PMC1221787 fatcat:6wzqrsxhvzfepogk33lo5fdt24

Identification of enhancer-like elements defines regulatory networks active in planarian adult stem cells [article]

Jakke Neiro, Divya Sridhar, Anish Dattani, Aziz Aboobaker
2022 bioRxiv   pre-print
Planarians have become an established model system to study regeneration and stem cells, but the regulatory elements in the genome remain almost entirely undescribed.  ...  Our work identifies active enhancers regulating adult stem cells and regenerative mechanisms.  ...  Homologs were then searched for the TFs with BLAST, and the planarian literature was reviewed to assign screened TFs to previously described.  ... 
doi:10.1101/2022.02.03.479047 fatcat:f6veitdhnzb2fp6c45qeq6t45u

Tools for targeted manipulation of the mouse genome

Louise van der Weyden, David J. Adams, Allan Bradley
2002 Physiological Genomics  
structures, and expression sites) and the Mammalian Gene Collection [MGC; who provide a complete set of full-length (open reading frame) sequences and cDNA clones of human and mouse genes (233) ].  ...  The second component uses paired-end whole-genome shotgun reads to generate light (ϳ2.5-fold) and deeper (5to 6-fold) coverage of the mouse genome; the sequence is obtained by preparing plasmid libraries  ... 
doi:10.1152/physiolgenomics.00074.2002 pmid:12464689 fatcat:dtwp25sn6jbehfrahjfbvs2ufi

Advances and opportunities in gene editing and gene regulation technology for Yarrowia lipolytica

Vijaydev Ganesan, Michael Spagnuolo, Ayushi Agrawal, Spencer Smith, Difeng Gao, Mark Blenner
2019 Microbial Cell Factories  
Metabolic engineering of this non-conventional yeast started through conventional molecular genetic engineering tools; however, recent advances in gene/genome editing systems, such as CRISPR-Cas9, transposons  ...  , and TALENs, has greatly expanded the applications of synthetic biology, metabolic engineering and functional genomics of Y. lipolytica.  ...  The resulting strategy, therefore, uses six sgRNAs to target each open reading frame in the genome.  ... 
doi:10.1186/s12934-019-1259-x pmid:31783869 pmcid:PMC6884833 fatcat:ngcb2b3ehrbexk326dxx4bsldy

De novo gene birth

Stephen Branden Van Oss, Anne-Ruxandra Carvunis
2019 PLoS Genetics  
Acknowledgments We thank Aaron Wacholder for his careful reading of and feedback on draft manuscripts.  ...  In the same year, however, Pierre-Paul Grassé coined the term "overprinting" to describe the emergence of genes through the expression of alternative open reading frames (ORFs) that overlap preexisting  ...  On homology searches by protein Blast and the characterization of the age of genes.  ... 
doi:10.1371/journal.pgen.1008160 pmid:31120894 pmcid:PMC6542195 fatcat:5tflrryw5ff35lhb3yaohta35a
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