Results 1 - 10 of 41

MIPS: a database for genomes and protein sequences

by H. W. Mewes, D. Frishman, U. Gildener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Minsterkötter, S. Rudd, B. Weil - Nucleic Acids Res , 2002
"... The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually a ..."
Abstract - Cited by 336 (10 self) - Add to MetaCart
., 28, 155-158; Barker et aL (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res

by Gary H. Van Domselaar, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, Anchi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russ Greiner, David S. Wishart , 2005
"... BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and hyper-link ..."
Abstract - Cited by 67 (5 self) - Add to MetaCart
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and hyper

KOBAS server: a web-based platform for automated annotation and pathway identification

by Jianmin Wu, Xizeng Mao, Tao Cai, Jingchu Luo, Liping Wei - Nucleic Acids Res , 2006
"... There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experi-ments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously demon ..."
Abstract - Cited by 54 (7 self) - Add to MetaCart
There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experi-ments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously

RNA polymerase III transcribes human microRNAs.

by Glen M Borchert , William Lanier , Beverly L Davidson - Nature Struct. Mol. Biol. , 2006
"... Prior work demonstrates that mammalian microRNA (miRNA or miR) expression requires RNA polymerase II (Pol II). However, the transcriptional requirements of many miRNAs remain untested. Our genomic analysis of miRNAs in the human chromosome 19 miRNA cluster (C19MC) revealed that they are intersperse ..."
Abstract - Cited by 201 (3 self) - Add to MetaCart
. RESULTS miRNAs localize to repeats within the human genome We expanded prior studies by screening sequences flanking all known human miRNAs for repetitive elements (500 bp upstream and down stream) and annotating them using the Censor web server at the Genetic Information Research Institute 13 . Overall

Genome analysis WebGBrowse—a web server for GBrowse

by Ram Podicheti, Rajesh Gollapudi, Qunfeng Dong , 2009
"... Summary: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload ..."
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Summary: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users

Genome analysis CGAS: comparative genomic analysis server

by Masumi Itoh, Hidemi Watanabe
"... Summary: Comparative approach is one of the most essential methods for extracting functional and evolutionary information from genomic sequences. So far, a number of sequence comparison tools have been developed, and most are either for on-site use, requiring program installation but providing a wid ..."
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wide variety of analyses, or for the online search of user’s sequences against given databases on a server. We newly devised an Asynchronous JavaScript and XML (Ajax)-based system for comparative genomic analyses, CGAS, with highly interactive interface within a browser, requiring no software

Map-Reduce Expansion of the ISGA Genomic Analysis Web Server

by Chris Hemmerich, Adam Hughes, Yang Ruan, Aaron Buechlein, Judy Qiu, Geoffrey Fox
"... Abstract — Biological sequence data can be subjected to a variety of analysis workflows to glean pertinent scientific insight. Recent advances in sequencing techniques have led to a deluge of biosequence data, which necessitates the use of high-performance computing resources in order to carry out a ..."
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of these genome annotation servers, Integrative Services for Genomics Analysis (ISGA), and then describes a simple extension to the underlying workflow system that leverages the powerful Twister Iterative Map-Reduce runtime for streamlined dataparallel job control and enhanced access to clusters, grids, and Cloud

MEGANTE: A Web-Based System for Integrated Plant Genome Annotation

by Hisataka Numa, Takeshi Itoh , 2013
"... The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable in-crease in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and kn ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting

GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining

by Marco Masseroli, Dario Martucci, Francesco Pinciroli - Nucleic Acids Res , 2004
"... Statistical and clustering analyses of gene expression results from high-density microarray experiments produce lists of hundreds of genes regulated differentially, or with particular expression profiles, in the conditions under study. Independent of the microarray platforms and analysis methods use ..."
Abstract - Cited by 45 (3 self) - Add to MetaCart
of genes, most of them do not give methods for evaluating the relevance of the annotations provided, or for estimating the functional bias introduced by the gene set on the array used to identify the gene list considered. We developed Genome Functional INtegrated Discoverer (GFINDer), a web server able

Genome analysis RNATOPS-W: a web server for RNA structure searches of genomes

by Yingfeng Wang, Zhibin Huang, Yong Wu, Russell L. Malmberg, Liming Cai, Ivo Hofacker , 2009
"... Summary: RNATOPS-W is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS, a command line C++ software package ..."
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Summary: RNATOPS-W is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS, a command line C++ software
Results 1 - 10 of 41