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In this issue

Entrez Programming Utilities (E-Utils)

PubChem

GenePlot

New NLM Catalog in Entrez

New Genome Builds

New Microbial Genomes in GenBank

Whole Genome Shotgun Project

Web BLAST

Trace Archive Grows

New Organisms in UniGene

RefSeq Version 8

Submissions Corner

Predicted Records

GenBank Release 144

BLAST 2.2.10

Publications

Masthead





New Genome Builds and Annotations at NCBI

Human Reference Genome Build 35 Version 1

The NCBI Map Viewer now shows Version 1 of NCBI's annotation on the reference human genome build 35. Sequences for two alternatives to the reference assembly's Major Histocompatibility Complex DR51 haplotype, DR52 and DR53, are included in this build.

The Map Viewer also displays, on the “Celera” assembly tracks, the December 2001 whole genome shotgun assembly (WGSA) generated by Celera from 27 million reads of Celera's 5.3X whole genome shotgun data and 104,000 BAC end sequence pairs from GenBank. The Map Viewer shows the alignment of RefSeq RNAs to the Celera genome assembly on the “gene_seq” track, however, GenBank mRNAs and ESTs were not aligned to genomic contigs from Celera, nor were Gnomon predictions made.

The method used to convert sequence coordinates to cytogenetic bands has been changed for Build 35.1 and is described in Furey and Haussler D.1
New maps include a Repeats track showing the alignment of repetitive elements detected by RepeatMasker2. Also new are the Gallus gallus UniGene map showing the alignment of mRNAs from UniGene clusters and the EST map showing the alignment of mRNAs and ESTs.

Mouse Reference Genome, Build 33 Version 1

The Map Viewer now shows mouse Build 33 Version 1 that is based on data available as of June 18, 2004, and includes 25,874 mapped genes. Build 33 was assembled using HTGS phase 3 sequence, single fragment HTGS phase 2 sequence and the MGSCv3. A tiling path was hand-curated by combining data from clone based Tiling Path Files (TPFs) and the MGSCv3. The Sanger Center's nearly-complete assembly for chromosome 11 is also presented.

New Tracks appearing in Map Viewer include a Repeats track similar to that described above, a Rat UniGene track showing alignment of rat mRNAs, labeled according to the UniGene cluster to which they belong, a Rat EST track, and a track showing CpG islands identified using the algorithm described in Takai and Jones.3

Chicken Build 1, Version 1 in Map Viewer

The NCBI Map Viewer now displays NCBI's assembly of chicken genomic sequence data along with genetic and physical maps. Assemblies for chromosomes 25, 29 through 31, and 33 through 38 are not yet available. Four linkage groups that have not yet been mapped to any chromosome are also represented.

Mouse Genome Sequencing Consortium

1. Hum Mol Genet. 2003 May 1;12(9):1037-44. PMID: 12700172

2. Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0.
1996-2004 <http://www.repeatmasker.org>

3. Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3740-5. PMID: 11891299

Continue to:  New Microbial Genomes in GenBank

NCBI News | Fall/Winter 2002 NCBI News: Spring 2003