TITLE

ASAP: Amplification, sequencing & annotation of plastomes

PUB. DATE
January 2005
SOURCE
BMC Genomics;2005, Vol. 6, p176
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
No abstract available.
ACCESSION #
43683939

 

Related Articles

  • ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Glasner, Jeremy D.; Rusch, Michael; Liss, Paul; Plunkett, Guy; Cabot, Eric L.; Darling, Aaron; Anderson, Bradley D.; Infield-Harm, Paul; Gilson, Michael C.; Perna, Nicole T. // Nucleic Acids Research;Jan2006, Vol. 34 Issue suppl 1, pd41 

    ASAP is a comprehensive web-based system for community genome annotation and analysis. ASAP is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences. New tools, such as the genome alignment program...

  • ASAP, a systematic annotation package for community analysis of genomes. Glasner, Jeremy D.; Liss, Paul; Plunkett III, Guy; Darling, Aaron; Prasad, Tejasvini; Rusch, Michael; Byrnes, Alexis; Gilson, Michael; Biehl, Bryan; Blattner, Frederick R.; Perna, Nicole T. // Nucleic Acids Research;Jan2003, Vol. 31 Issue 1, p147 

    ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization (https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm). ASAP facilitates ongoing...

  • The Complete Chloroplast Genome of Coix lacryma-jobi and a Comparative Molecular Evolutionary Analysis of Plastomes in Cereals. Leseberg, Charles H.; Duvall, Melvin R. // Journal of Molecular Evolution;Oct2009, Vol. 69 Issue 4, p311 

    Graminoid molecular evolution was investigated by chloroplast genome (plastome) scale analyses. A complete plastome from Coix lacryma-jobi (Poaceae) and a draft plastome from Joinvillea plicata (Joinvilleaceae) were sequenced and analyzed. The draft plastome included conserved protein-coding...

  • ASAP: the Alternative Splicing Annotation Project. Lee, Christopher; Atanelov, Levan; Modrek, Barmak; Xing, Yi // Nucleic Acids Research;Jan2003, Vol. 31 Issue 1, p101 

    Recently, genomics analyses have demonstrated that alternative splicing is widespread in mammalian genomes (30–60% of genes reported to have multiple isoforms), and may be one of their most important mechanisms of functional regulation. However, by comparison with other genomics data such...

  • Resolving deep relationships of PACMAD grasses: a phylogenomic approach. Cotton, Joseph L.; Wysocki, William P.; Clark, Lynn G.; Kelchner, Scot A.; Chris Pires, J.; Edger, Patrick P.; Mayfield-Jones, Dustin; Duvall, Melvin R. // BMC Plant Biology;Jul2015, Vol. 15 Issue 1, p1 

    Background: Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12...

  • Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae). Naumann, Julia; Der, Joshua P.; Wafula, Eric K.; Jones, Samuel S.; Wagner, Sarah T.; Honaas, Loren A.; Ralph, Paula E.; Bolin, Jay F.; Maass, Erika; Neinhuis, Christoph; Wanke, Stefan; de Pamphilis, Claude W. // Genome Biology & Evolution;Feb2016, Vol. 8 Issue 2, p345 

    Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present...

  • Updating annotations with the distributed annotation system and the automated sequence annotation pipeline. Speier, William; Ochs, Michael F. // Bioinformatics;Nov2012, Vol. 28 Issue 21, p2858 

    Summary: The integration between BioDAS ProServer and Automated Sequence Annotation Pipeline (ASAP) provides an interface for querying diverse annotation sources, chaining and linking results, and standardizing the output using the Distributed Annotation System (DAS) protocol. This interface...

  • The evolution of chloroplast genes and genomes in ferns. Wolf, Paul; Der, Joshua; Duffy, Aaron; Davidson, Jacob; Grusz, Amanda; Pryer, Kathleen // Plant Molecular Biology;Jun2011, Vol. 76 Issue 3-5, p251 

    Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some...

  • Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP. Dugas, Diana V.; Hernandez, David; Koenen, Erik J.M.; Schwarz, Erika; Straub, Shannon; Hughes, Colin E.; Jansen, Robert K.; Nageswara-Rao, Madhugiri; Staats, Martijn; Trujillo, Joshua T.; Hajrah, Nahid H.; Alharbi, Njud S.; Al-Malki, Abdulrahman L.; Sabir, Jamal S. M.; Bailey, C. Donovan // Scientific Reports;11/27/2015, p16958 

    The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily...

  • Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison. Mariotti, Roberto; Cultrera, Nicolò G. M.; Díez, Concepcion Muñoz; Baldoni, Luciana; Rubini, Andrea // BMC Plant Biology;2010, Vol. 10, p211 

    Background: The cultivated olive (Olea europaea L.) is the most agriculturally important species of the Oleaceae family. Although many studies have been performed on plastid polymorphisms to evaluate taxonomy, phylogeny and phylogeography of Olea subspecies, only few polymorphic regions...

Share

Other Topics