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Anaplasma marginale major surface protein 3 is encoded by a polymorphic, multigene family
1997
Infection and Immunity
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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
2018
PeerJ
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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]
2017
bioRxiv
pre-print
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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]
2002
Functional Genomics
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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
2015
Nucleic Acids Research
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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
2015
Molecular Genetics and Genomics
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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]
2008
Lecture Notes in Computer Science
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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
2011
Nature Methods
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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
2021
Genes
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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
2000
Bioinformatics
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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
2001
Biochemical Journal
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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]
2022
bioRxiv
pre-print
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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
2002
Physiological Genomics
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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
2019
Microbial Cell Factories
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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
2019
PLoS Genetics
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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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