Comparative Genomics: assembly, alignment and annotation
Comparative genomics and transcriptomics in Saccharomyces
... Chapter 4 114 Raw data came with errors and needed to be preprocessed before being fed into downstream analyses like mapping or assembly. Basic tasks such as adapter removal, duplicate quantification and summary ...
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Assembly and repeat annotation of the nothobranchius furzeri genome
... its alignment to the reference with the equation 𝐾 = −1/2 ln (1 − 2𝑝 − 𝑞) − 1/4 ln (1 − 2𝑞) (where 𝑝 is the proportion of sites with transitions and 𝑞 is the proportion of sites with ...the alignment output ...
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Comparative genomics of bacteriophage of the genus Seuratvirus
... Abstract Despite being more abundant and having smaller genomes than their bacterial host, relatively few bacteriophages have had their genomes sequenced. Here, we isolated 14 bacteriophages from cattle slurry and ...
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Genome Annotation and Comparative Genomics of ORF Virus
... genome annotation, an individual gene and its protein (or RNA) product can be predicted by in depth analysis of several gene features, such as ORFs length, % (G + C) content, promoter, polyA tail, homology, ...
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A Comparative Genomics Pipeline for In Silico Characterization and Functional Annotation of Short Hypothetical Proteins
... of comparative genomics, wide phylogenetic distribution and in- dispensability for cell growth have been taken into consideration by some researchers when choosing uncharacterized genes for experimental ...
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Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic archaeon DL31
... III. RESULTS AND DISCUSSION The comparative genomic studies for characterizing 991 genes of Unclassified Halophilic archaeon DL31 was done. The classifications of proteins were done by using sequence similarity ...
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Aldo-keto reductase (AKR) superfamily: Genomics and annotation
... sequence alignment and degree of identity. Annotation of non-vertebrate AKRs at the National Center for Biotechnology Information or Vertebrate Genome Annotation (vega) database does not often ...
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Comparative genomics of the skin Staphylococci
... PacBio assembly of the J31 genome was different from each of these groups with both region 2a and 2b being located as a single ...PacBio assembly indicates that regions 2a and 2b are fused whereas the ...
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Comparative Genomics of Carp Herpesviruses
... the alignment includes the entire coding region of the ORF151D protein, the C-terminal regions of carp JunB and the ORF151C protein, and the N-terminal region of the ORF151B ...
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Comparative genomics of Brassica oleracea
... novo assembly of the short (~150bp) sequence reads into large contigs, and eventually chromosomes, is beyond current computational capabilities unless some framework is available to reduce the ...
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The Microbe browser for comparative genomics
... and annotation data, continuously updated and extended with automated and manual anno- tation in UniProtKB ...mize annotation, but they also modify gene sequences, changing translational start site ...
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Comparative genomics and chromosome evolution
... In order to test whether differences were present at a more local level, we next compared normalized one Mb intra-bin Hi-C contacts between the two species, again using the M. muntjak assembly as the backbone for ...
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Structure and assembly cues of Arabidopsis root-inhabiting bacterial communities and comparative genomics of selected Rhizobium members
... In this study a high-resolution methodology based on pyrosequencing of the bacterial 16S rRNA marker gene was adopted to characterize and compare soil and root-inhabiting bacterial communities. Our results show that ...
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An improved oil palm genome assembly as a valuable resource for crop improvement and comparative genomics in the Arecoideae subfamily
... Oil palm and coconut are estimated to have diverged from date palm around 62.5 million year ago [ 31 ]. Fission or fusion of two chromosomes into one or vice versa is known in many lineages [ 48 ]; this event is observed ...
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Comparative Study on Annotation Techniques
... automatic annotation approach proposed. Automatic annotation approach consist of three ...is alignment phase, second is annotation phase and third is annotation wrapper generation ...1: ...
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Virome assembly and annotation: A surprise in the Namib Desert
... However, comparative analyses assessing the efficiency of these procedures are still outstanding. Despite severe environmental constraints, deserts host a multitude of animals, plants, and microorganisms, and are ...
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Comparative Genomics of Enterococcus Faecium Bacteriophages
... 2014. Comparative analysis of the seprophages identified eight sequence types, which differed in size and gene ...on alignment analyses of the major functional proteins encoded in the prophage genomes ...
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Comparative Genomics and Metabolomics in the Genus Nocardia
... The gene clusters organized in GCF 4 are also found in all Nocardia species. Here, a single NRPS with four modules is colocated with a putative N-acyltransferase and two transporters. The produced peptide likely consists ...
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Comparative genomics and the nature of placozoan species
... maximum gaps per read, 2,000-bp maximum single gap size, and 24-bp word length. Overlap- ping contigs were again checked for identical AUGUSTUS gene models. In the case of missing annotation on both sequences, ...
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Protein domain evolution by comparative genomics
... Chapter 2. Domain Assignment 81 2.4 C onclusion 2.4.1 D om ain A ssign m en t P rotocols This domain assignment protocol shows a great deal of promise for the widespread and wholesale autom ated annotation of ...
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