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RefSeq - Wikipedia, the free encyclopedia 
 
en.wikipedia.org/wiki/RefSeq
The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products.    
 
 
NCBI Reference Sequences (RefSeq): current status, new ... 
 
www.ncbi.nlm.nih.gov/pubmed/22121212
1. Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5. doi: 10.1093/nar/gkr1079. Epub 2011 Nov 24. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.  
 
 
 
Home - Gene - NCBI 
 
https://www.ncbi.nlm.nih.gov/gene
A portal to gene-specific content based on NCBI's RefSeq project, information from model organism databases, and other resources. In addtion to the rich content of the database, Gene provides a wealth of links to resources with additional information    
 
 
RefSeq: NCBI Reference Sequence Database 
 
www.wip.ncbi.nlm.nih.gov/refseq
Announcements January 7, 2015 RefSeq Release 69 is available for FTP. This release includes: Proteins 52,276,468 Transcripts 9,973,568 Organisms 51,661  
 
 
 
GenBank, RefSeq, TPA and UniProt: What’s in a Name? 
 
www.microbemagazine.org/...refseq-tpa...in-a-name&Itemid...
GenBank, RefSeq, TPA and UniProt: What’s in a Name? The National Center for Biotechnology Information often is asked about the differences between its GenBank, RefSeq, and TPA databases and how they relate to the UniProt database.  
 
 
 
Refseq Database Lncrna Gene Annotation | lncRNA Blog 
 
www.lncrnablog.com/search/refseq-database-lncrna-gene...
Cancer is a disease of aberrant gene expression. Genome-wide association studies in cancer reveal that more than 80% of cancer-associated SNPs (single-nucleotide polymorphism) occur in noncoding regions of the genome.  
 
 
 
Publications - RefSeq: NCBI Reference Sequence Database 
 
www.wip.ncbi.nlm.nih.gov/refseq/publications
Citing RefSeq. When using the RefSeq database, please cite one of the following: The NCBI handbook [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2002 Oct. Chapter 18, The Reference Sequence (RefSeq) Project.  
 
 
 
UniProt, GeneID, RefSeq mapping: how does it work? 
 
www.uniprot.org/help/ncbi_mappings
How does UniProt do GeneID and RefSeq mappings? As per a protocol we have formalized with the NCBI, we create a RefSeq protein centric-mapping.    
 
 
National Center for Biotechnology Information - Wikipedia ... 
 
en.wikipedia.org/wiki/National_Center_for_Biotechnology...
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.  
 
 
 
Accession Number - AccessionNumber < FIG < NMPDR 
 
www.nmpdr.org/FIG/wiki/view.cgi/FIG/AccessionNumber
Accession Number . An accession number is a unique identifier assigned to a particular genome or protein sequence? to uniquely identify it in a database.  
 
 
 
Convert Refseq Id To Gene Name 
 
https://www.biostars.org/p/73272
I'm trying to convert a list of RefSeq IDs to the Gene Symbol. . . I can do it for Ensembl using http://genome.ucsc.edu/cgi-bin/hgTables [Track -> Ensembl Genes : Table -> ensemblToGeneName]    
 
 
Convert Refseq Accession To Gene Symbol Using Biomart 
 
https://www.biostars.org/p/13390
Hi, I've several refseq id that I want to convert to gene symbol. So in R with biomaRt : librar...    
 
 
Refseq 
 
wn.com/refseq
Searching for Nucleotide Sequences: Reference Sequences (RefSeq), RefSeqGene, Downloading RefSeq Genes from UCSC Table Browser (Greek), Downloading RefSeq Genes from Ensembl-Biomart (Greek), 遺伝子のRefSeq IDを調べる 2011    
 
 
NCBI Reference Sequence (RefSeq): a curated non-redundant ... 
 
nar.oxfordjournals.org/content/33/suppl_1/D501.full?...
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins  
 
 
 
18. The Reference Sequence ( RefSeq ) Project 
 
www.plantsciences.ucdavis.edu/BIT150/2006/JD_Lecture/...
Kim Pruitt, et al. The Reference Sequence (RefSeq) Project. 18-2 include attribution to the original sequence data; however, RefSeq differs from GenBank in the  
 
 
 
Data formats - Ensembl Genome Browser 
 
www.ensembl.org/info/docs/tools/vep/vep_formats.html
The VEP can use VCF, pileup and HGVS notations in addition to the default format. Default. The default format is a simple whitespace-separated format (columns may be separated by space or tab characters) ... REFSEQ_MATCH - the RefSeq transcript match status; ...  
 
 
 
OpenHelix: RefSeq 
 
www.openhelix.com/cgi/tutorialInfo.cgi?id=120
RefSeq, and similar projects with ties to RefSeq, continue to provide quality, reviewed, reference sequences for a variety of projects. RefSeq data can be found in many bioinformatics tools. You will learn: The history and framework for RefSeq ;  
 
 
 
Refseq -- a curated non-redundant sequence database of ... 
 
www.hsls.pitt.edu/obrc/index.php?page=URL1043765470
NCBI's Reference Sequence (RefSeq) database is a curated non-redundant collection of sequences representing genomes, transcripts and proteins.  
 
 
 
RefSeq - CLAB 
 
biodoc.ist.unomaha.edu/wiki/RefSeq
--Bknelson 05:05, 14 June 2010 (UTC) Creation of an mpiformatdb database 1. Refseq files (.gbff.gz and .gpff.gz) are downloaded from Bio-Mirror using rsync to specific directories based on type  
 
 
 
Entrez Gene Database 
 
jura.wi.mit.edu/entrez_gene/sample_queries.php
Given A Specific RefSeq Gene Id, Select General Information; Given A Specific Gene Id, Select GO Terms; Given A Species And Gene Symbol, Select General Information. What is the gene symbol and chromosome of a specific gene id? This is a simple query on one table.  
 
 
 
About RefSeq : NCBI Reference Sequence Database 
 
0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/refseq/about
About RefSeq. The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.  
 
 
 
RefSeq: YP_004475149 
 
www.genome.jp/dbget-bin/www_bget?refseq:YP_004475149
LOCUS YP_004475149 125 aa linear CON 17-DEC-2014 DEFINITION flagellar protein FliS [Pseudomonas fulva 12-X]. ACCESSION YP_004475149 VERSION YP_004475149.1 GI:333901276 DBLINK BioProject: PRJNA67351 DBSOURCE REFSEQ: accession NC_015556.1 KEYWORDS ...  
 
 
 
NLM Technical Bulletin, Sep–Oct 2006, RefSeq Accession ... 
 
www.nlm.nih.gov/pubs/techbull/so06/so06_refseq.html
RefSeq Accession Numbers in MEDLINE ® a ccession numbers for the Reference Sequence (RefSeq) collection are now being added to MEDLINE records when a journal article reports that new data has been added to that database.  
 
 
 
RefSeq - University at Buffalo Libraries 
 
libweb.lib.buffalo.edu/pdp/index.asp?ID=334
Description. The RefSeq - Reference Sequence provides a comprehensive, curated, integrated, non-redundant (one record for each gene, or each splice variant, from each organism represented) set of sequences, including genomic DNA, transcript (RNA), and protein products.  
 
 
 
RefSeq Curator with Computercraft Corporation | 356028 
 
jobs.sciencecareers.org/job/356028/refseq-curator
Computercraft seeks a highly motivated individual who will use his or her biological expertise to define RefSeq sequence standards and to contribute to functional annotation of both the sequence records and the companion resource, NCBI’s Gene database.  
 
 
 
Thoughts on converting gene identifiers - Musings from a PhD ... 
 
davetang.org/.../11/25/thoughts-converting-gene-identifiers
Some thoughts on converting gene identifiers from different gene annotation databases.  
 
 
 
RefSeq Genes: Updated to NCBI Provided Alignments and Why You ... 
 
blog.goldenhelix.com/grudy/refseq-genes-updated-to-ncbi...
You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product.  
 
 
 
HGVS recommendations: reference sequence 
 
www.hgvs.org/mutnomen/refseq.html
Reference sequence descriptions. To indicate what type of reference sequence is used for the description of the sequence variant, specific indicators are used;  
 
 
 
Refseq Lincrna Database | lncRNA Blog 
 
www.lncrnablog.com/search/refseq-lincrna-database
Arraystar is going to launch Arraystar Mouse LncRNA Expression Microarray V3.0! This array is designed for the global profiling of mouse long noncoding RNAs (LncRNAs).  
 
 
 
RefSeq and LocusLink: NCBI gene-centered resources 
 
nar.oxfordjournals.org/content/29/1/137.full
RefSeq. RefSeq transcript and corresponding protein records are now produced through two independent processes. The first process, which relies heavily on manual curation, provides a non-redundant dataset of transcripts and proteins of known genes for human ...  
 
 
 
hORFeome V8.1 Library | Broad Institute of MIT and Harvard 
 
www.broadinstitute.org/rnai/orfs
The link below provides the latest information on the composition of the hORFeome V8.1 Entry and Expression Libraries produced at the Broad Institute in collaboration with the Dana-Farber Cancer Institute Center for Cancer Systems ... do not perfectly match one unique NCBI RefSeq transcript.    
 
 
Comparative Analysis - California State University, Stanislaus 
 
cogs.csustan.edu/~tom/bioinfo-S03/ppt/day5.ppt
RefSeq sequences are not submitted primary sequences. RefSeq records are owned by NCBI and therefore can be updated as needed to maintain current annotation or to incorporate additional sequence information.  
 
 
 
DAVID: functional annotation result summary 
 
david.abcc.ncifcrf.gov/conversion.jsp
Gene ID Conversion Tool: DAVID Bioinformatics Resources 6.7, NIAID/NIH: Home; Start Analysis; Shortcut to DAVID Tools; Technical Center; Downloads & APIs; Term of Service; Why DAVID? About Us; Functional Annotation - Functional Annotation Clustering  
 
 
 
Mapping proteomics data to UniProt, RefSeq and gene symbols 
 
www.cureffi.org/2013/03/...to-uniprot-refseq-and-gene-symbol...
Mapping proteomics data to UniProt, RefSeq and gene symbols. Mar 15, 2013 • ericminikel. update: this post was substantially revised on 2013-03-18 to correctly handle different isoforms of proteins  
 
 
 
RefSeq Gene - University of Washington 
 
mrhgsv.gs.washington.edu/cgi-bin/hgc?hgsid=1049543&o=......
Description. The RefSeq Genes track shows known protein-coding genes taken from the NCBI mRNA reference sequences collection (RefSeq). On assemblies in which incremental GenBank downloads are supported, the data underlying this track are updated nightly.  
 
 
 
Welcome to EcoGene-RefSeq | EcoGene-RefSeq 
 
www.ecogene.org/refseq/node/1
EcoGene-RefSeq A collection of EcoGene Tools for RefSeq Prokaryotic Genomes Main menu. Home; Genomes; Switch Genome Welcome to EcoGene-RefSeq, ...  
 
 
 
NCBI reference sequences (RefSeq): a curated non-redundant ... 
 
www.researchgate.net/publication/6668660_NCBI_reference...
Publication » NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.  
 
 
 
qPrimerDepot 
 
mouseprimerdepot.nci.nih.gov
This database provides qRT PCR primers for all mouse RefSeq sequences. For 99% of intron-bearing genes, the PCR product will cross an exon-exon border which overlaps one of the largest introns.    
 
 
Overview : Main : Sequence Read Archive : NCBI/NLM/NIH 
 
trace.ncbi.nlm.nih.gov/Traces/sra
In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. SRA is NIH’s primary archive of high-throughput sequencing data and is part of the international partnership of archives (INSDC) at the NCBI, the European ...    
 
 
qPrimerDepot 
 
primerdepot.nci.nih.gov
This database provides qRT PCR primers for 99.96% human RefSeq sequences. For 99% of intron-bearing genes, the PCR product will cross an exon-exon border which overlaps one of the largest introns.    
 
 
DNA Methylation Promoter Arrays - EpiGenie 
 
epigenie.com/products/dna-methylation-promoter-arrays
DNA Methylation Promoter Arrays. EpiGenie | Epigenetics, Stem Cell, ... 3x720K CpG Island Plus RefSeq Promoter Arrays are multiplex slides with 3 identical arrays per slide enabling the simultaneous analysis of 3 DNA Methylation samples for increased sample throughput.  
 
 
 
CHO-K1 RefSeq - CHOGenome.org 
 
www.chogenome.org/search_refseq_cho.php
Your query may take up to one minute, depending on the number of hits in the assembly database. This is a BETA version of the CHO-K1 RefSeq genome database.  
 
 
 
RefSeq: an update on mammalian reference sequences ... 
 
www.researchgate.net/publication/258825158_RefSeq_an...
Publication » RefSeq: an update on mammalian reference sequences..  
 
 
 
UCSC Genome Browser discussion forum () 
 
comments.gmane.org/gmane.science.biology.ucscgenome...
Hi UCSC Genome Browser friends, I am writing to ask a very common question about converting refseq id to gene symbol. One solution is to look for the mapping in the kgXref table.  
 
 
 
A comprehensive evaluation of ensembl, RefSeq, and UCSC ... 
 
www.biomedcentral.com/1471-2164/16/97
Research article A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification  
 
 
 
how to retrieve UCSC refseq genes in R bioconductor - Stack ... 
 
stackoverflow.com/...ucsc-refseq-genes-in-r-bioconductor
I am analyzing some ChIP-seq data and I was able to retrieve the sequence element associated with each chipped chromosomal region using the genome browser. After parsing and searching for specific  
 
 
 
RefSeq Curator : Bethesda, MD, United States : Naturejobs 
 
www.nature.com/naturejobs/science/jobs/498781-refseq-curator...
RefSeq Curator - Computercraft Corporation are looking for a Staff Scientist in Bethesda, MD, United States. Salary: unspecified, Hours: Full-time, Type: Permanent  
 
 
 
entrez ID conversion - SEQanswers 
 
seqanswers.com/forums/showthread.php?t=9390
Hello, does anyone know how to convert entrez I.D. to either Refseq ID or Gene Symbols? I have found resources on Refseq to Gene Symbol conversion, but I can't find anything on Entrez I.D.  
 
 
 
Portal towards Databases and Sites related to Genetics ... 
 
atlasgeneticsoncology.org/extdef.html
GDB : The Genome Database An international collaboration in support of the Human Genome Entrez_Gene Entrez_Gene is a part of Entrez devoted to search informations on genes and links to other database as RefSeq, maps, OMIM, Unigene, Pubmed....  
 
 
 
RefSeq - ICGEB 
 
www.icgeb.res.in/whotdr/cd1/PreCourseReading/NAR_DB2003/...
Database Description. RefSeq provides curated non-redundant sequence standards for genomic regions, transcripts (including splice variants), and proteins.  
 
 
 


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