TPFs are loaded to a centralized system for tracking. This system also manages QA on the files as an ongoing process. The first level of QA is to look at the overlap between adjacent sequences on the TPF.
When certifying an overlap, external evidence supporting the alignment must be available. Evidence typically consists of sequence data from another source, spanning clone ends or experimental verification (such as a PCR assay detecting the join).These certificates are reviewed by other GRC members and may be approved or rejected. Certification information is publicly available.
Alignments refer to pairs of sequence. Once you know how a pair of sequences go together, you can look at stringing the pairs along into a contig. The contig is essentially the consensus sequence that is produced from the components.To create a contig, we use the steps shown on this slide.What are switch points? As you create the consensus sequence of the contig, the switch points tell you where to stop using the sequence from one component and begin using the sequence from the next.
Church gmod2012 pt1
The Evolution of the Resources Navigating Genome Reference Human Genome at NCBI Part 1 Deanna M. Church, NCBI@deannachurch
ClinVar 140,000 2,500,000 GTR Twenty Two Years of Growth: Genome Remapping Service PubMed Health CloneDB 120,000 NCBI Data and User Services Public Access Genome Decoration Page Influenza Seqs. GenBank Base Pairs GenSAT 2,000,000 Users (Average) GeneTests PubChem Peptidome 100,000 Trace Archive BioSystems CCDS Flu H1N1 Cancer Chromosomes Environmental Samples Discovery Initiative 1,500,000Base Pairs (Millions) 80,000 PubMed Central Entrez Genes Entrez Sensors Users/Weekday BLINK Mouse Composite Primer BLAST MapViewer Genome GEO Gnomon Seq Read Archive GeneRIFs UniSTS WGS RefSeqGene 60,000 HLA Haplotypes Human Genome Human Genome-TPA Genome Reference LinkOut Consortium 1,000,000 dbMHC dbVar PubMed LocusLink Epigenomics BookShelf PSI-BLAST RefSeq MyNCBI BankIt Human Genome- VAST dbSNP 1000 Genomes 40,000 Genomes Transcripts Alignments ePCR Project Taxonomy Microbial Genomes Genome-Wide PHI-BLAST Association Studies 3D Structure OMIM CGAP dbGap 500,000 Network Entrez GeneMap Entrez Portal 20,000 Cn3D WWW GenBank UniGene dbSTS Entrez at NCBI BLAST dbEST 0 0 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
NCBITools Literature Data Blast PubMed GenBank GBench PubMed Central Protein DB Splign Bookshelf SRA Cn3D MeSH GEO e-PCR Gene Reviews dbSNPe-Utilities … Gene … RefSeq …
Entrez: Pathway to Discovery Term frequency statistics MEDLINE abstracts Literature Literature citations citations in in sequence sequence databases databases Nucleotide Protein sequences sequences Nucleotide Amino acid sequencesequence similarity Coding region similarity features
UGT2B17 MHC MAPT GRCh37 (hg19) 7 alternate haplotypes at the MHC Alternate loci released as: FASTA AGP Alignment to chromosomehttp://genomereference.org
Assembly (e.g. GRCh37)PAR Non-nuclear Primary assembly unit Assembly (e.g. MT) ALT ALT ALT Genomic 1 2 3 Region (MHC) Genomic ALT ALT ALT Region 4 5 6 (UGT2B17) Genomic Region ALT ALT (MAPT) 7 8 ALT 9
Richa AgarwalaMHC Alternate locus Alignment to chr6
Oh No! Not a new version of the human genome!http://genomereference.org
Assembly (e.g. GRCh37.p5)PAR Non-nuclear Primary assembly unit Assembly (e.g. MT) ALT ALT ALT Genomic 1 2 3 Region (MHC) Genomic ALT ALT ALT Region 4 5 6 (UGT2B17) Genomic Region ALT ALT (MAPT) 7 Genomic 8 Region (ABO) Genomic ALT Region 9 (SMA) Genomic Region (PECAM1) Patches …
TBC1D3C TBC1D3 TBC1D3H TBC1D3CMyo19 region (17q21)
60 Fix PATCHES: Chromosome will update in GRCh38 (adds >1 Mb of novel sequence to the assembly)70 Novel PATCHES: Additional sequence added (adds >800K of novel sequence to the assembly) Releasing patches quarterly
Distributed data Centralized Data Old Assembly Model Updated Assembly ModelGenome not in INSDC Database Genome in INSDC Database