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Databases of homologous gene families for comparative genomics

Simon Penel, Anne-Muriel Arigon, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, Laurent Duret, Manolo Gouy, Guy Perrière
2009 BMC Bioinformatics  
Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the  ...  In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable.  ...  We thank the IN2P3 (Villeurbanne) for the computing resources and Pascal Calvat for his technical help.  ... 
doi:10.1186/1471-2105-10-s6-s3 pmid:19534752 pmcid:PMC2697650 fatcat:my355rhj5fgcvm42ui4ej4xpau

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies

Shalabh Thakur, David S. Guttman
2016 BMC Bioinformatics  
Conclusion: DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes.  ...  The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range  ...  Consent for publication Not applicable. Ethics approval and consent to participate Not applicable.  ... 
doi:10.1186/s12859-016-1142-2 pmid:27363390 pmcid:PMC4929753 fatcat:q2dsnzmr4vf6lcft2wv2agqlle

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences

Yujun Han, James M. Burnette, Susan R. Wessler
2009 Nucleic Acids Research  
retrieve gene family homologs from a genomic database, (ii) characterize gene structure and (iii) perform phylogenetic analysis.  ...  Gene families compose a large proportion of eukaryotic genomes. The rapidly expanding genomic sequence database provides a good opportunity to study gene family evolution and function.  ...  In addition, the authors would like to thank Drs Hongyan Shan, Jim Leebens-Mack, Russell Malmberg and Yaowu Yuan for critical reading of the manuscript and for valuable discussions.  ... 
doi:10.1093/nar/gkp295 pmid:19429695 pmcid:PMC2699529 fatcat:howpzxyucvczbopu3tup6xsj5y

HOPPSIGEN: a database of human and mouse processed pseudogenes

K. Adel
2004 Nucleic Acids Research  
Moreover, the ancestral structure of processed pseudogenes could be easily inferred using the sequence of their functional homologous genes.  ...  Owing to these characteristics, processed pseudogenes represent good neutral markers for studying genome evolution.  ...  We used the c 2 -statistics to compare the number of sequences in each category for the two species: ***P < 10 À4 ; **P < 0.001; *P < 0.01; P > 0.01 (NS).  ... 
doi:10.1093/nar/gki084 pmid:15608268 pmcid:PMC540038 fatcat:wbaqpzsudjadzoq4kjy2rm5lxy

HOPPSIGEN: a database of human and mouse processed pseudogenes

K. Adel
2005 Nucleic Acids Research  
Moreover, the ancestral structure of processed pseudogenes could be easily inferred using the sequence of their functional homologous genes.  ...  Owing to these characteristics, processed pseudogenes represent good neutral markers for studying genome evolution.  ...  We used the c 2 -statistics to compare the number of sequences in each category for the two species: ***P < 10 À4 ; **P < 0.001; *P < 0.01; P > 0.01 (NS).  ... 
doi:10.1093/nar/gki217 pmcid:PMC546172 fatcat:yub7x6hdivcqllsth7flekrrla

Genome cartography through domain annotation

C P Ponting, N J Dickens
2001 Genome Biology  
To account for the great diversity of domain contexts and an unexpected paucity of ortholog conservation, we must categorize the coding regions of completely sequenced genomes into domain families, as  ...  The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes.  ...  Tools and databases Homology from the Jackson Laboratory for the comparison of mammalian genomes.  ... 
pmid:11521679 fatcat:57ewcgr5obautgpysl3afg45ci

Aequatus: an open-source homology browser

Anil S Thanki, Nicola Soranzo, Javier Herrero, Wilfried Haerty, Robert P Davey
2018 GigaScience  
Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as  ...  as the conservation of ancestral exon boundaries amongst multiple genomes.  ...  For a selected gene, homologues are fetched from homology and homology member tables of the Ensembl Compara database.  ... 
doi:10.1093/gigascience/giy128 pmid:30395211 pmcid:PMC6251984 fatcat:ft4xlirnufhbnady4qwrzlk2um

Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

D. W.A. Buchan
2002 Genome Research  
This system attempts to assign genes to their related InterPro/CluSTr families and store all available information; they also provide a range of comparative genomics tools for their analyzed genomes.  ...  For example, although the genome annotation resource GeneQuiz lists structural relatives for about 10% of the genes in the yeast genome, there are no direct links to structural families.  ... 
doi:10.1101/gr.213802 pmid:11875040 pmcid:PMC155287 fatcat:ezk254prz5e4dbnj2nocux3bua

Studies on fungal Pumilio gene family through mining multiple genome-scale data sets

Yutaka Matsushima, Reiko Sugiura, Takayoshi Kuno
2007 The Kobe journal of medical sciences  
In S. pombe genome, nine genes belonging to Pumilio gene family were found and were clustered into four groups by homology of their amino acid sequences.  ...  The genes belonging to Pumilio gene family of the fission yeast Schizosaccharomyces pombe (S. pombe) were compared with genome information of the several fungi and their functions have been inferred using  ...  Search for orthologues of the Pumilio gene family of S. pombe in the fungal genomes. SGD TM Saccharomyces Genome Database was used for S. cerevisiae (budding yeast).  ... 
pmid:17932456 fatcat:2e4mfqczuvfibc4r7x6ds4tvru

Synergistic use of plant-prokaryote comparative genomics for functional annotations

Svetlana Gerdes, Basma El Yacoubi, Marc Bailly, Ian K Blaby, Crysten E Blaby-Haas, Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Jeffrey C Waller, Andreas Wilke, Ross Overbeek, Andrew D Hanson (+1 others)
2011 BMC Genomics  
In-depth comparative genomic analysis was performed for 360 top candidate families.  ...  Computer-assisted selection of promising targets for deeper analysis was based on homology-independent characteristics associated in the SEED database with the prokaryotic members of each family.  ...  We thank Brian Haas for help and advice in identifying Arabidopsis gene families having three or fewer members, and Skip Fournier and Wayne Decatur for rRNA analysis in yeast.  ... 
doi:10.1186/1471-2164-12-s1-s2 pmid:21810204 pmcid:PMC3223725 fatcat:hbop5ctl7rfunjjv3hgstjpt7y

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics

Junyang Yue, Jiacheng Liu, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei (+2 others)
2020 Horticulture Research  
The database currently contains all publicly available genome and gene sequences, gene annotations, biochemical pathways, transcriptome profiles derived from public RNA-Seq datasets, and comparative genomic  ...  Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species.  ...  Acknowledgements This study was supported by grants from the National Natural Science Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1038/s41438-020-0338-9 pmid:32821400 pmcid:PMC7395147 fatcat:hrkefpgi2vdgdpv233fuqse75q

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse

J. A. Blake
2000 Nucleic Acids Research  
for genes and alleles, incorporates links to other genomic resources such as sequence data, and includes a variety of additional information about the laboratory mouse.  ...  The Mouse Genome Database (MGD) is a comprehensive public database of mouse genomic, genetic and phenotypic information (http://www.informatics.jax.org ).  ...  Homology and comparative genomics Mammalian gene orthologs are of great interest to researchers. In MGD, most mammalian homology data comes from peerreviewed publications.  ... 
doi:10.1093/nar/28.1.108 pmid:10592195 pmcid:PMC102449 fatcat:ktxj23y7izcjxprc5733y4lvve

GreenPhylDB v5: a comparative pangenomic database for plant genomes

Guignon Valentin, Toure Abdel, Droc Gaëtan, Dufayard Jean-François, Conte Matthieu, Rouard Mathieu
2020 Nucleic Acids Research  
GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important  ...  With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several  ...  We also acknowledge community databases which provided access to the genome datasets, thus facilitating the development of this online resource. FUNDING  ... 
doi:10.1093/nar/gkaa1068 pmid:33237299 fatcat:5mlzhivrn5ewhm3ymev7y5pfhm

Extent of Gene Duplication in the Genomes of Drosophila, Nematode, and Yeast

Zhenglong Gu, Andre Cavalcanti, Feng-Chi Chen, Peter Bouman, Wen-Hsiung Li
2002 Molecular biology and evolution  
At any rate, it is clear that the genome of Drosophila melanogaster has undergone few gene duplications in the recent past and has much fewer gene families than C. elegans.  ...  We conducted a detailed analysis of duplicate genes in three complete genomes: yeast, Drosophila, and Caenorhabditis elegans.  ...  Stahl for discussion. The comments of the two reviewers and the computer support from R. Blocker are greatly appreciated. LITERATURE CITED  ... 
doi:10.1093/oxfordjournals.molbev.a004079 pmid:11861885 fatcat:7jqohoe5wfbt7pugmdeq66wble

Unique genes in giant viruses: Regular substitution pattern and anomalously short size

H. Ogata, J.-M. Claverie
2007 Genome Research  
Large DNA viruses, including giant mimivirus with a 1.2-Mb genome, exhibit numerous orphan genes possessing no database homologs or genes with homologs solely in close members of the same viral family.  ...  Second, position-dependent nucleotide statistics were similar between family-specific genes and the remaining genes in the genome.  ...  Van Etten for giving us an early access to the genome sequence data of NY2A (GenBank DQ491002). We thank Adam Monier for critical reading of the manuscript.  ... 
doi:10.1101/gr.6358607 pmid:17652424 pmcid:PMC1950904 fatcat:frakr3ocyjhxrgjvvlc5k6pvaa
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