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Articles by R Durbin
Total Records ( 2 ) for R Durbin
  H Li , B Handsaker , A Wysoker , T Fennell , J Ruan , N Homer , G Marth , G Abecasis , R Durbin and 1000 Genome Project Data Processing Subgroup
 

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.

  K. D Pruitt , J Harrow , R. A Harte , C Wallin , M Diekhans , D. R Maglott , S Searle , C. M Farrell , J. E Loveland , B. J Ruef , E Hart , M. M Suner , M. J Landrum , B Aken , S Ayling , R Baertsch , J Fernandez Banet , J. L Cherry , V Curwen , M DiCuccio , M Kellis , J Lee , M. F Lin , M Schuster , A Shkeda , C Amid , G Brown , O Dukhanina , A Frankish , J Hart , B. L Maidak , J Mudge , M. R Murphy , T Murphy , J Rajan , B Rajput , L. D Riddick , C Snow , C Steward , D Webb , J. A Weber , L Wilming , W Wu , E Birney , D Haussler , T Hubbard , J Ostell , R Durbin and D. Lipman
 

Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers. Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy. To date, the project has identified 20,159 human and 17,707 mouse consensus coding regions from 17,052 human and 16,893 mouse genes. Three evaluation methods indicate that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS. The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions.

 
 
 
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