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Current status and new features of the Consensus Coding Sequence database

Catherine M. Farrell, Nuala A. O'Leary, Rachel A. Harte, Jane E. Loveland, Laurens G. Wilming, Craig Wallin, Mark Diekhans, Daniel Barrell, Stephen M. J. Searle, Bronwen Aken, Susan M. Hiatt, Adam Frankish (+31 others)
2013 Nucleic Acids Research  
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of proteincoding regions that are identically annotated on the human and  ...  We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites.  ...  ACKNOWLEDGEMENTS The authors wish to thank the programmers, database and curation staff at Ensembl, NCBI, HAVANA and UCSC for their contributions to the CCDS analysis, maintenance and continuing curation  ... 
doi:10.1093/nar/gkt1059 pmid:24217909 pmcid:PMC3965069 fatcat:go2bm4timjdhzc6ecp42w77k7m

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

K. D. Pruitt, T. Tatusova, G. R. Brown, D. R. Maglott
2011 Nucleic Acids Research  
We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline  ...  The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links  ...  The Consensus Coding Sequence collaboration [http://www .ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi (9) ] is a central hub for curation of protein-coding loci and all members must agree to updates  ... 
doi:10.1093/nar/gkr1079 pmid:22121212 pmcid:PMC3245008 fatcat:n2exzcnlwbfi7ef24fcdeyuaca

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E Berry, Eric Cox (+25 others)
2017 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors wish to thank all programmers and other staff at NCBI, EMBL-EBI, UCSC, HGNC and MGI, who contributed to CCDS analyses and maintenance of the CCDS database and its internal  ...  The authors also thank UniProtKB curators, scientific experts and CCDS users for their helpful inputs. FUNDING  ...  The Consensus Coding Sequence (CCDS) collaboration was formed in 2005 to address the issue of discrepancies between Ensembl and NCBI genome annotations by producing a consensus dataset of protein-coding  ... 
doi:10.1093/nar/gkx1031 pmid:29126148 pmcid:PMC5753299 fatcat:xlfpwnmezjejtbg7dyatdwspvi

Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank

Allison Piovesan, Maria Caracausi, Marco Ricci, Pierluigi Strippoli, Lorenza Vitale, Maria Chiara Pelleri
2015 DNA Research  
Remarkably, this size is indeed consistent with the sum of the splicing consensus sequence lengths.  ...  The structuring of the data, the creation of additional calculation fields and the integration with nucleotide sequences allow users to make many types of comparisons and calculations that are useful for  ...  Funding This work was funded by 'RFO' grants from Alma Mater Studiorum-University of Bologna to P.S. and L.V. M.C.'s and A.P.'  ... 
doi:10.1093/dnares/dsv028 pmid:26581719 pmcid:PMC4675715 fatcat:ho5uaaypnjh4ba5idne5ddiyjy

The current status and portability of our sequence handling software

Rodger Staden
1986 Nucleic Acids Research  
I describe the current status of our sequence analysis software.  ...  The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use.  ...  A program DBAUTO takes the data passed on from the screening programs, calculates a consensus for the current state of the project database, and then compares each new gel reading in turn with the consensus  ... 
doi:10.1093/nar/14.1.217 pmid:3511446 pmcid:PMC339382 fatcat:32fs6g3fhfbw3let6n4ghu3hji

Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes

T. Wylie
2004 Nucleic Acids Research  
Nematode.net currently provides NemaGene EST cluster consensus sequence, enhanced online BLAST search tools, functional classifications of cluster sequences and comprehensive information concerning the  ...  The database is an outgrowth of the parasitic nematode EST project at Washington University ' s Genome Sequencing Center (GSC), St Louis.  ...  Addi tional useful features of nematode.net include summaries of sequence status for all nematode species, cDNA library descriptions, project specifics, >300 organized nematology links and a trace viewer  ... 
doi:10.1093/nar/gkh010 pmid:14681448 pmcid:PMC308745 fatcat:alqmlkbvfng3zm36kcgfknephu

Tracking and coordinating an international curation effort for the CCDS Project

R. A. Harte, C. M. Farrell, J. E. Loveland, M.-M. Suner, L. Wilming, B. Aken, D. Barrell, A. Frankish, C. Wallin, S. Searle, M. Diekhans, J. Harrow (+1 others)
2012 Database: The Journal of Biological Databases and Curation  
Here, we present the current status of the CCDS database and details on our procedures to track and coordinate our efforts.  ...  The Consensus Coding Sequence (CCDS) collaboration involves curators at multiple centers with a goal of producing a conservative set of high quality, protein-coding region annotations for the human and  ...  Acknowledgements We wish to thank the programmers, database and curation staff at Ensembl, NCBI, WTSI and UCSC for their contribution to the CCDS analysis, maintenance and continuing curation efforts.  ... 
doi:10.1093/database/bas008 pmid:22434842 pmcid:PMC3308164 fatcat:3rppcgpcovf7deqvave3x3lafe

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

Oleksiy Kohany, Andrew J Gentles, Lukasz Hankus, Jerzy Jurka
2006 BMC Bioinformatics  
In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct  ...  Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments.  ...  Acknowledgements Development of Censor was supported by National Institutes of Health grant 5 P41 LM006252-08. We would like to thank Jolanta Walichiewicz for help with preparing the manuscript.  ... 
doi:10.1186/1471-2105-7-474 pmid:17064419 pmcid:PMC1634758 fatcat:jqktrodvjrfvdb7bxyalwvddle

Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data

Paul A Christensen, Sishir Subedi, Kristi Pepper, Heather L Hendrickson, Zejuan Li, Jessica S Thomas, S Wesley Long, Randall J Olsen
2020 JAMIA Open  
Materials and Methods We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1.  ...  Results We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors.  ...  This window displays the version status for each external database. The status consists of a number (months passed since its release date) and a color code (green ¼ 0-1 year, yellow ¼ 1-2 years, red !  ... 
doi:10.1093/jamiaopen/ooaa004 pmid:32734171 pmcid:PMC7382636 fatcat:vmg6icvbzve4boeakjgrv7syua

RiTE database: a resource database for genus-wide rice genomics and evolutionary biology

Dario Copetti, Jianwei Zhang, Moaine El Baidouri, Dongying Gao, Jun Wang, Elena Barghini, Rosa M. Cossu, Angelina Angelova, Carlos E. Maldonado L., Stefan Roffler, Hajime Ohyanagi, Thomas Wicker (+12 others)
2015 BMC Genomics  
The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive  ...  The database allows sequence browsing, downloading, and similarity searches.  ...  Funding This work was supported by the National Science Foundation Plant Genome Award (grant number 1026200) to RAW & SAJ; and both the Bud Antle and AXA Endowed Chairs to RAW. 4 Center for Applied Genetic  ... 
doi:10.1186/s12864-015-1762-3 pmid:26194356 pmcid:PMC4508813 fatcat:ksdsmgtkyzgwthwbmewcf7pxjq

GeneNest: automated generation and visualization of gene indices

Stefan A Haas, Tim Beissbarth, Eric Rivals, Antje Krause, Martin Vingron
2000 Trends in Genetics  
The comprehensive database of consensus sequences that summarize every putative transcript is an efficient tool for searching homologies to private sequences and avoids searching of multiple sequence databases  ...  Genomics 1, 281-291 12 Hofmann, K. (1999) The PROSITE database, its status in 1999.  ... 
doi:10.1016/s0168-9525(00)02116-8 pmid:12199289 fatcat:7owq456im5aifpbrba3utwc6ri

Bioinformatics methods for the analysis of hepatitis viruses

Francesco Moriconi, Michael R Beard, Lilly KW Yuen
2013 Antiviral Therapy  
Acknowledgements The work carried out to develop the SeqHepC database was supported by a grant from the Australian Centre for HIV and Hepatitis Virology Research (collaborative network of principal investigators  ...  Disclosure statement The authors declare no competing interests.  ...  [15] , the genotype, subtype and drugnaive status could be confirmed for 228 of the HCV full-length genome sequences analysed using the data available in the Los Alamos HCV Sequence Database and the  ... 
doi:10.3851/imp2613 pmid:23792814 fatcat:mjndishfd5bvvhugh6xwaua6im

A new DNA sequence assembly program

James K. Bonfield, Kathryn F. Smith, Rodger Staden
1995 Nucleic Acids Research  
The program provides many visual clues to the current state of a sequencing project and allows users to interact in intuitive and graphical ways with their data.  ...  The program is suitable for large and small projects, a variety of strategies and can handle data from a range of sequencing instruments.  ...  We are also grateful to Simon Dear for work done when a member of the group. We also thank Molly Craxton, Alan Bankier and Tony Crowther for critical reading of the manuscript.  ... 
doi:10.1093/nar/23.24.4992 pmid:8559656 pmcid:PMC307504 fatcat:ggdgyrwv5bgs5crj7w7uafguhy

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

K. D. Pruitt, T. Tatusova, D. R. Maglott
2007 Nucleic Acids Research  
RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features.  ...  The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence  ...  ACKNOWLEDGEMENTS This work was supported by the Intramural Research Program of the NIH, National Library of Medicine.  ... 
doi:10.1093/nar/gkl842 pmid:17130148 pmcid:PMC1716718 fatcat:t7rciayrzncfnmxhdp44hjk76a

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

Allison Piovesan, Maria Caracausi, Francesca Antonaros, Maria Chiara Pelleri, Lorenza Vitale
2016 Database: The Journal of Biological Databases and Curation  
We are grateful to Kirsten Welter for her kind and expert revision of the manuscript.  ...  We thank all the other people that very kindly contributed by individual donations to support part of the fellowships as well as hardware and software.  ...  The available RefSeq statuses associated with genes and the corresponding RNAs are summarized in Supplementary Table S1 ; it should be noted that the RefSeq status of a particular RNA may be different  ... 
doi:10.1093/database/baw153 pmid:28025344 pmcid:PMC5199132 fatcat:mrbpticihvekfal3jpdot62vxi
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