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82
MIPS: analysis and annotation of proteins from whole genomes
- Nucleic Acids Res
, 2004
"... resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of.400 genomes automatically annotated w ..."
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Cited by 206 (14 self)
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computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein– protein interactions or other types
MIPS: a database for genomes and protein sequences
- 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
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Cited by 336 (10 self)
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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
MIPS: analysis and annotation of genome information in 2007
- Nucleic Acids Research
, 2008
"... combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to ortholo ..."
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Cited by 23 (0 self)
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combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known
Analysis of Antisense Expression by Whole Genome Tiling Microarrays and siRNAs Suggests Mis-Annotation of Arabidopsis Orphan Protein-Coding Genes
"... Background: MicroRNAs (miRNAs) and trans-acting small-interfering RNAs (tasi-RNAs) are small (20–22 nt long) RNAs (smRNAs) generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expressio ..."
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whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans) and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with sm
A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis
- PLoS ONE
, 2008
"... Background. Diatoms are unicellular algae responsible for approximately 20 % of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids. Methodology/Principal Findings. The whole genome sequen ..."
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Cited by 23 (2 self)
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sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization
Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins, 2nd edn
, 2001
"... As discussed earlier in this book, GenBank was created in response to the explosion in sequence information resulting from a panoply of scientific efforts such as the Human Genome Project. To review, GenBank is an annotated collection of all pub-licly available DNA and protein sequences and is maint ..."
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Cited by 77 (2 self)
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As discussed earlier in this book, GenBank was created in response to the explosion in sequence information resulting from a panoply of scientific efforts such as the Human Genome Project. To review, GenBank is an annotated collection of all pub-licly available DNA and protein sequences
Simultaneous Alignment and Annotation
"... Annotation is clearly a central problem in comparative genomics: You use observed molecular evolution to make statements about something you can’t observe, such as a folding RNA molecule or the protein gene structure in a genome segment. Alignment is more a nuisance problem that must be solved befor ..."
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Annotation is clearly a central problem in comparative genomics: You use observed molecular evolution to make statements about something you can’t observe, such as a folding RNA molecule or the protein gene structure in a genome segment. Alignment is more a nuisance problem that must be solved
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
- PLoS Comput. Biol
, 2009
"... Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large pub ..."
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Cited by 35 (2 self)
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Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large
CAAT-Box, Contigs-Assembly and Annotation tool-box for genome sequencing projects. Bioinformatics 20:790–797
, 2004
"... Motivation: Contigs-Assembly and Annotation Tool-Box (CAAT-Box) is a software package developed for the computa-tional part of a genome project where the sequence is obtained by a shotgun strategy. CAAT-Box contains new tools to predict links between contigs by using similarity searches with other w ..."
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Cited by 21 (8 self)
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whole genome sequences. Most importantly, it allows annota-tion of a genome to commence during the finishing phase using a gene-oriented strategy. For this purpose, CAAT-Box creates an Individual Protein file (IPF) for each ORF of an assembly. The nucleotide sequence reported in an IPF corresponds
EA: Evidencebased annotation of the malaria parasite's genome using comparative expression profiling
- Plouffe D, Henson K, Nussenzweig V, Carlton J, Vinetz JM, Duraisingh MT, Winzeler
"... A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla or are phylumspecific. This problem is especially acute in pathogens, such a ..."
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Cited by 16 (0 self)
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A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla or are phylumspecific. This problem is especially acute in pathogens
Results 1 - 10
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82
