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The UCSC Genome Browser Database.

Karolchik, D Baertsch, R Diekhans, M Furey, Ts Hinrichs, A Lu, Yt Roskin, Km Schwartz, M Sugnet, Cw Thomas, Dj ...

Published in Nucleic Acids Research

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and q...

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. PDF available through Get Fulltext Research

Smith, Am Heisler, Le St Onge, Rp Farias-Hesson, E Wallace, Im Bodeau, J Harris, An Perry, Km Giaever, G Nader Pourmand ...

Published in Nucleic Acids Research

Next-generation sequencing has proven an extremely effective technology for molecular counting applications where the number of sequence reads provides a digital readout for RNA-seq, ChIP-seq, Tn-seq and other applications. The extremely large number of sequence reads that can be obtained per run permits the analysis of increasingly complex samples...

The UCSC Genome Browser database: 2014 update. PDF available through Get Fulltext Research

Karolchik, D Barber, Gp Casper, J Clawson, H Cline, Ms Diekhans, M Dreszer, Tr Fujita, Pa Guruvadoo, L Haeussler, M ...

Published in Nucleic Acids Research

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser s web-based tools provide an integrated environment for ...

The UCSC Proteome Browser.

Hsu, F Pringle, Th Kuhn, Rm Karolchik, D Diekhans, M David Haussler Kent, Wj

Published in Nucleic Acids Research

The University of California Santa Cruz (UCSC) Proteome Browser provides a wealth of protein information presented in graphical images and with links to other protein-related Internet sites. The Proteome Browser is tightly integrated with the UCSC Genome Browser. For the first time, Genome Browser users have both the genome and proteome worlds at t...

A hidden Markov model that finds genes in E. coli DNA.

Krogh, A Mian, Is David Haussler

Published in Nucleic Acids Research

A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes states that model the codons and their frequencies in E. coli genes, as well as the patterns found in the intergenic region, including repetitive extragenic...

A hidden Markov model that finds genes in E. coli DNA.

Krogh, A Mian, Is David Haussler

Published in Nucleic Acids Research

A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes states that model the codons and their frequencies in E. coli genes, as well as the patterns found in the intergenic region, including repetitive extragenic...

The UCSC Genome Browser database: 2016 update. PDF available through Get Fulltext Research

Harte, Ra Haeussler, M Guruvadoo, L Fujita, Pa Eisenhart, C Diekhans, M Clawson, H Casper, J Barber, Gp David Haussler ...

Published in Nucleic Acids Research

For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its incepti...

The UCSC Genome Browser database: 2014 update. PDF available through Get Fulltext Research

Karolchik, D Barber, Gp Casper, J Clawson, H Cline, Ms Diekhans, M Dreszer, Tr Fujita, Pa Guruvadoo, L Haeussler, M ...

Published in Nucleic Acids Research

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser s web-based tools provide an integrated environment for ...

The UCSC Genome Browser database: 2014 update. PDF available through Get Fulltext Research

Karolchik, D Barber, Gp Casper, J Clawson, H Cline, Ms Diekhans, M Dreszer, Tr Fujita, Pa Guruvadoo, L Haeussler, M ...

Published in Nucleic Acids Research

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser s web-based tools provide an integrated environment for ...

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

Todd Lowe Eddy, Sr

Published in Nucleic Acids Research

We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This...

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