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A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Daniel G Pinheiro, Pedro AF Galante, Sandro J de Souza, Marco A Zago, Wilson A Silva
2009 BMC Bioinformatics  
In this work, we present a web-based tool named S3T: Score System for Sequence Tags, to index sequenced tags in accordance with their reliability.  ...  High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent  ...  Acknowledgements The authors would like to thank all members of the Laboratory of Molecular Genetics and Bioinformatics for their contributions during the development phase and further, for the feedback  ... 
doi:10.1186/1471-2105-10-170 pmid:19500384 pmcid:PMC2701951 fatcat:d4mw6bjrjje6lmd447nbrxnxfy

Unicycler: resolving bacterial genome assemblies from short and long sequencing reads [article]

Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt
2016 biorxiv/medrxiv   pre-print
Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective.  ...  Unicycler utilises a novel semi-global aligner, which is used to align long reads to the assembly graph.  ...  Semi-global long-read alignment While short reads can resolve repeats up to the insert size of the library (typically <1000 bp), long reads provide a much more powerful source of scaffolding information  ... 
doi:10.1101/096412 fatcat:fibbfptvljdbzfobdeeikd2l3y

The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont

Kristina K Gagalova, Justin G A Whitehill, Luka Culibrk, Diana Lin, Véronique Lévesque-Tremblay, Christopher I Keeling, Lauren Coombe, Macaire M S Yuen, Inanç Birol, Jörg Bohlmann, Steven J M Jones
2022 G3: Genes, Genomes, Genetics  
Pissodes strobi, commonly known as the spruce weevil or white pine weevil, is a major pest of spruce and pine forests in North America.  ...  Here we describe the nuclear and mitochondrial P. strobi genomes and their annotations, as well as the genome of an apparent Wolbachia endosymbiont.  ...  Graham for the support with the phylogenomics analysis and Vincent Desrosiers, Plateforme de cytométie du Centre de Recherche du Chu de Québec, for assistance with the flow cytometry.  ... 
doi:10.1093/g3journal/jkac038 pmid:35171977 pmcid:PMC8982425 fatcat:zpo7bft4znebteasfbbfeojufu

History and Future Perspectives of Barley Genomics

Kazuhiro Sato
2020 DNA Research  
For the future project, an efficient annotation pipeline is essential for establishing the function of genomes and genes as well as for using this information for sequence-based digital barley breeding  ...  The long-term goal of this project is to analyze the genome sequences of major barley accessions worldwide.  ...  Acknowledgments The author thanks the National Bioresource Project, Japan, for collection, preservation and distribution of barley resources stored at Okayama University described in this review.  ... 
doi:10.1093/dnares/dsaa023 pmid:32979265 pmcid:PMC7532727 fatcat:wfs26twovvf2fcit4csykc7xnu

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt, Adam M. Phillippy
2017 PLoS Computational Biology  
Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective.  ...  Unicycler uses a novel semi-global aligner to align long reads to the assembly graph.  ...  Semi-global long-read alignment While short reads can resolve repeats up to the insert size of the library (typically <1000 bp), long reads provide a much more powerful source of scaffolding information  ... 
doi:10.1371/journal.pcbi.1005595 pmid:28594827 pmcid:PMC5481147 fatcat:uzfxjqtcifbr5hwvncga75ipw4

Genetic Alterations in Mitochondrial DNA Are Complementary to Nuclear DNA Mutations in Pheochromocytomas

Mouna Tabebi, Małgorzata Łysiak, Ravi Kumar Dutta, Sandra Lomazzi, Maria V. Turkina, Laurent Brunaud, Oliver Gimm, Peter Söderkvist
2022 Cancers  
Material: To determine the potential roles of mtDNA alterations in sporadic PCCs/PGLs, we analyzed a panel of 26 nuclear susceptibility genes and the entire mtDNA sequence of seventy-seven human tumors  ...  Results: Our results revealed that 53.2% of the tumors harbor a mutation in at least one of the targeted susceptibility genes, and 16.9% harbor complementary mitochondrial mutations.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cancers14020269 pmid:35053433 pmcid:PMC8773562 fatcat:stm36i26lvg3fi4bfa6r6cmcpy

The crossover from microscopy to genes in marine diversity: from species to assemblages in marine pelagic copepods

Silke Laakmann, Leocadio Blanco-Bercial, Astrid Cornils
2020 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Copepods are known for their high taxonomic and ecological diversity and comprise a huge variety of behaviours, forms and life histories, making them a highly interesting and well-studied group in terms  ...  Furthermore, their short life cycles and rapid responses to changing environments make them good indicators and core research components for ecosystem health and status in the light of environmental change  ...  This review is a product of SCOR Working Group MetaZooGene (WG157) and Working Group on Integrated Morphological and Molecular Taxonomy (WGIMT) of the International Council for the Exploration of the Sea  ... 
doi:10.1098/rstb.2019.0446 pmid:33131432 fatcat:fejkpwhuibgurdkkshhuw7ecfu

Large-Scale Discovery and Characterization of Protein Regulatory Motifs in Eukaryotes

Daniel S. Lieber, Olivier Elemento, Saeed Tavazoie, Sridhar Hannenhalli
2010 PLoS ONE  
We estimate that ,80% of these are novel predictions in that they do not match a known motif in both sequence and biological context, suggesting that post-translational regulation of protein behavior is  ...  These predicted motifs, many of which display preferential association with specific biological pathways and non-random positioning in the linear protein sequence, provide focused hypotheses for experimental  ...  Acknowledgments We thank Hani Goodarzi, Alison Hottes and other members of the Tavazoie lab for their helpful comments.  ... 
doi:10.1371/journal.pone.0014444 pmid:21206902 pmcid:PMC3012054 fatcat:ib3d7v54mbervdkzsecilqvuqe

Positively-Charged Semi-Tunnel Is a Structural and Surface Characteristic of Polyphosphate-Binding Proteins: An In-Silico Study

Zheng Zachory Wei, Greg Vatcher, Alvin Hok Yan Tin, Jun Lin Teng, Juan Wang, Qing Hua Cui, Jian Guo Chen, Albert Cheung Hoi Yu, Eugene A. Permyakov
2015 PLoS ONE  
Here we proposed a putative polyP binding site, a positively-charged semi-tunnel (PCST), identified by surface electrostatics analyses in polyP kinases (PPKs) and many other polyP-related proteins.  ...  Molecular docking calculations revealed a significant value for binding affinity to polyP in PCST-containing proteins.  ...  Michael Yaoyao YIN, Yi Nan ZHANG and Xiao Jing MA for assistance in data analyses. This project was started by Arthur Kornberg and continued in his memory.  ... 
doi:10.1371/journal.pone.0123713 pmid:25879219 pmcid:PMC4400040 fatcat:7zheymlyxze6nn5wieildmndgm

Platform AI: Cryoelectron Microscopy & Reconstruction

2008 Biophysical Journal  
This implies that C. elegans can develop into a system to study the molecular and genetic basis of KCNE-mediated muscle contractility and disease states.  ...  The proposed semi-interactive approach avoids the long run-times and the sensitivity to noise of fully-automatic segmentation methods, and is at the same time -due to the automatic local search -less subjective  ...  Analysis of 5 0 -flanking sequence to exon 0 revealed a promoter region with multiple vicinal start sites, a TATA sequence for transcriptional regulation and the presence of a quasiperfect estrogen responsive  ... 
doi:10.1016/s0006-3495(08)79097-0 fatcat:cwda7r53ergwbhstxvlndhsq2e

Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602

Thomas Schafhauser, Daniel Wibberg, Antonia Binder, Christian Rückert, Tobias Busche, Wolfgang Wohlleben, Jörn Kalinowski
2022 Journal of Fungi  
Two alleles of biosynthetic gene clusters for pleuromutilin were found in the genome of C. passeckerianus.  ...  In accordance with the dikaryotic state of the fungus, the nuclear genome has a diploid character. Interestingly, the mitochondrial genome appears duplicated.  ...  The combination of long-read (Nanopore) and short-read (Illumina) sequencing improved base accuracy and significantly reduced error rates in the final genome.  ... 
doi:10.3390/jof8080862 pmid:36012850 pmcid:PMC9410065 fatcat:l7z7ttlia5h4bhzh5als22ci6a

Genome annotation

Sébastien Aubourg, Pierre Rouzé
2001 Plant physiology and biochemistry (Paris)  
The annotation work is divided into two steps: structural annotation, which consists mainly of localizing gene elements; and functional annotation, which aims at assigning a biochemical function to the  ...  For scientists, the challenge is to exploit this huge amount of sequences. To extract biological knowledge from anonymous genomic sequences is the main objective of genome annotation.  ...  We would like to thank Raquel Tavares, Jeroen Raes and Martine De Cock for helpful comments and critical reading of the manuscript.  ... 
doi:10.1016/s0981-9428(01)01242-6 fatcat:sv45eyu6bbcllo3bik3rfvvbh4

Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Maria Aleksandra Bitner, Bernard L. Cohen
2015 Zoological Journal of the Linnean Society  
Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 1218 nucleotides of aligned sequences of the cox1 mitochondrial gene from 14 laqueoid  ...  signal) in the long-looped terebratulids.  ...  may be termed 'modified' long loops are currently placed in multiple superfamilies, the interrelationships of which are addressed here for the first time with gene sequence data (Fig. 6) ; however, more  ... 
doi:10.1111/zoj.12217 fatcat:4llwn2ogrzaczbjosjft23u4pa

Differentiating Pigs from Wild Boars Based on NR6A1 and MC1R Gene Polymorphisms

Anna Koseniuk, Grzegorz Smołucha, Małgorzata Natonek-Wiśniewska, Anna Radko, Dominika Rubiś
2021 Animals  
Along the MC1R gene sequence, we identified four polymorphic loci comprising three codons. The "wild type" allele was primarily found in wild boar but also in the Duroc and Złotnicka White breeds.  ...  We recommend that a larger sample of genomes is studied to verify this method.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ani11072123 fatcat:e5quev5y5vh2baty4vdovniqeq

Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology

Petr Soukal, Štěpánka Hrdá, Anna Karnkowska, Rafał Milanowski, Jana Szabová, Miluše Hradilová, Hynek Strnad, Čestmír Vlček, Ivan Čepička, Vladimír Hampl
2021 Scientific Reports  
Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns,  ...  R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis.  ...  Acknowledgements All sequencing and the salaries of VH and PS were financially supported by the Czech Science Foundation project nr. 13  ... 
doi:10.1038/s41598-021-92174-3 pmid:34158556 fatcat:fuakfttb7zer5pjv2u3o3n5554
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