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OrfPredictor: predicting protein-coding regions in EST-derived sequences
- Nucleic Acids Res
, 2005
"... OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it pre ..."
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Cited by 58 (2 self)
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OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. OrfPredictor is available at
Artemis and ACT: viewing, annotation and comparing sequences stored in relational database
- Bioinformatics
, 2008
"... stored in a relational database ..."
Complete Genome Sequence of the Prototype Lactic Acid Bacterium
, 2006
"... Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 ps ..."
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Cited by 44 (6 self)
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Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category “carbohydrate metabolism and transport, ” by far the largest category of novel proteins in comparison with L. lactis subsp. lactis IL1403. Nearly one-fifth of the 71 insertion elements are concentrated in a specific 56-kb region. This integration hot-spot region carries genes that are typically associated with lactococcal plasmids and a repeat sequence specifically found on plasmids and in the “lateral gene transfer hot spot ” in the genome of Streptococcus thermophilus. Although the parent of L. lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis MG1363 carries four remnant/satellite phages and two apparently complete prophages. The availability of the L. lactis MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research. Lactococcus lactis, a mesophilic fermentative bacterium producing lactic acid from sugar (hexose) fermentation, is an important
Introduction and summary
- Social Security Programs and Retirement around the World: Micro-Estimation. National Bureau of Economic research
, 2004
"... respiratory syncytial (RS) virus. The status of GP1 has been uncertain, because a cellular glycoprotein migrates at the same position when Laemmli's discontinuous buffer system is used for PAGE, and because BSC-1 cells infected with the RSN-2 strain of RS virus appear not to contain GP1. Howeve ..."
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Cited by 44 (3 self)
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respiratory syncytial (RS) virus. The status of GP1 has been uncertain, because a cellular glycoprotein migrates at the same position when Laemmli's discontinuous buffer system is used for PAGE, and because BSC-1 cells infected with the RSN-2 strain of RS virus appear not to contain GP1. However, additional evidence suggests that GP1 is a viral structural protein. (i) It is removed from cells by trypsin, while the cellular glycoprotein is not; (ii) it is separated from the cellular glycoprotein when the infected cells are analysed by neutral SDS-PAGE; (iii) it is present in the purified RSN-2 strain of RS virus produced by BSC-1 cells; (iv) it is also present in the purified Long strain of RS virus produced by either human or monkey cells. When purified Long strain virus is analysed by PAGE under non-reducing conditions, the glycoproteins VGP48 and GP26 migrate together, and VPM27 separates into two proteins, which one-dimensional peptide mapping suggests are not different proteins. These observations suggest that VGP48 and GP26 exist in the virion as a single molecule joined by disulphide bonds, and so resemble a paramyxovirus fusion protein, and that probably there are two forms of VPM27 which differ in either position or number of disulphide bonds.
Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35: D468–471
, 2007
"... The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has prompted the Saccharomyces Genome Database (SGD; ..."
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Cited by 43 (1 self)
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The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has prompted the Saccharomyces Genome Database (SGD;
CryptoDB: a Cryptosporidium bioinformatics resource update
- Page 8 of 9 article Database, Vol. 2012, Article ID bas007, doi:10.1093/database/bas007
, 2006
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Gramene, a bird’s eye view of cereal genomes
- Nucleic Acids Res
, 2006
"... Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind’s most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, ..."
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Cited by 32 (7 self)
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Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind’s most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999,
Eitinger T: Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters
- J Bacteriol
"... The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokar ..."
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Cited by 31 (3 self)
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The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokaryotes. For functional annotation of genes, we used two comparative genomic approaches: identification of regulatory signals and analysis of the genomic positions of genes encoding candidate nickel/cobalt transporters. The nickel-responsive repressor NikR regulates many nickel uptake systems, though the NikR-binding signal is divergent in various taxonomic groups of bacteria and archaea. B 12 riboswitches regulate most of the candidate cobalt transporters in bacteria. The nickel/cobalt transporter genes are often colocalized with genes for nickel-dependent or coenzyme B 12 biosynthesis enzymes. Nickel/cobalt transporters of different families, including the previously known NiCoT, UreH, and HupE/UreJ families of secondary systems and the NikABCDE ABC-type transporters, showed a mosaic distribution in prokaryotic genomes. In silico analyses identified CbiMNQO and NikMNQO as the most widespread groups of microbial transporters for cobalt and nickel ions. These unusual uptake systems contain an ABC protein (CbiO or NikO) but lack an extracytoplasmic solute-binding protein. Experimental analysis confirmed metal transport activity for three members of this family and demonstrated significant activity for a basic module (CbiMN) of the Salmonella enterica serovar Typhimurium transporter.
Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry
- J. Proteome Res. 2009
"... Additional resources and features associated with this article are available within the HTML version: • Supporting Information • Access to high resolution figures • Links to articles and content related to this article • Copyright permission to reproduce figures and/or text from this article ..."
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Cited by 25 (0 self)
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Additional resources and features associated with this article are available within the HTML version: • Supporting Information • Access to high resolution figures • Links to articles and content related to this article • Copyright permission to reproduce figures and/or text from this article
Prediction of subcellular localization using sequence-biased recurrent networks
- Bioinformatics
, 2005
"... doi:10.1093/bioinformatics/bti372 ..."
