Environmental shotgun sequencing promises to reveal novel and fundamental insights into the hidden world of microbes, but the complexity of analysis required to realize this potential poses unique interdisciplinary challenges.
+ }, + number = {3}, + doi = {10.1371/journal.pbio.0050082} +} + +@article{Sayers01012011, +author = {Sayers, Eric W. and Barrett, Tanya and Benson, Dennis A. and Bolton, Evan and Bryant, Stephen H. and Canese, Kathi and Chetvernin, Vyacheslav and Church, Deanna M. and DiCuccio, Michael and Federhen, Scott and Feolo, Michael and Fingerman, Ian M. and Geer, Lewis Y. and Helmberg, Wolfgang and Kapustin, Yuri and Landsman, David and Lipman, David J. and Lu, Zhiyong and Madden, Thomas L. and Madej, Tom and Maglott, Donna R. and Marchler-Bauer, Aron and Miller, Vadim and Mizrachi, Ilene and Ostell, James and Panchenko, Anna and Phan, Lon and Pruitt, Kim D. and Schuler, Gregory D. and Sequeira, Edwin and Sherry, Stephen T. and Shumway, Martin and Sirotkin, Karl and Slotta, Douglas and Souvorov, Alexandre and Starchenko, Grigory and Tatusova, Tatiana A. and Wagner, Lukas and Wang, Yanli and Wilbur, W. John and Yaschenko, Eugene and Ye, Jian}, +title = {Database resources of the National Center for Biotechnology Information}, +volume = {39}, +number = {suppl 1}, +pages = {D38-D51}, +year = {2011}, +doi = {10.1093/nar/gkq1172}, +URL = {http://nar.oxfordjournals.org/content/39/suppl_1/D38.abstract}, +eprint = {http://nar.oxfordjournals.org/content/39/suppl_1/D38.full.pdf+html}, +journal = {Nucleic Acids Research} +} + +@Article{RDogma, +AUTHOR = {Stacia K. Wyman, Robert K. Jansen and Jeffrey L. Boore}, +TITLE = {Automatic annotation of organellar genomes +with DOGMA}, +JOURNAL = {BIOINFORMATICS, oxford Press}, +VOLUME = {20}, +YEAR = {2004}, +NUMBER = {172004}, +PAGES = {3252-3255}, +URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004.pdf}, +} + +@article{de2002comparative, + title={Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns}, + author={De Las Rivas, Javier and Lozano, Juan Jose and Ortiz, Angel R}, + journal={Genome research}, + volume={12}, + number={4}, + pages={567--583}, + year={2002}, + publisher={Cold Spring Harbor Lab} +} + +@article{liu2012cpgavas, + title={CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences}, + author={Liu, Chang and Shi, Linchun and Zhu, Yingjie and Chen, Haimei and Zhang, Jianhui and Lin, Xiaohan and Guan, Xiaojun}, + journal={BMC genomics}, + volume={13}, + number={1}, + pages={715}, + year={2012}, + publisher={BioMed Central Ltd} +} + @article{parra2007cegma, title={CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes}, author={Parra, Genis and Bradnam, Keith and Korf, Ian}, @@ -53,6 +117,39 @@ DOI={10.1089/cmb.2010.0092} year={2004}, publisher={Cold Spring Harbor Lab} } + +@article{apweiler1985swiss, + title={SWISS-PROT AND ITS COMPUTER-ANNOTATED SUPPLEMENT TREMBL: HOW TO PRODUCE HIGH QUALITY AUTOMATIC ANNOTATION}, + author={Apweiler, Rolf and OâDonovan, Claire and Martin, Maria Jesus and Fleischmann, Wolfgang and Hermjakob, Henning and Moeller, Steffen and Contrino, Sergio and Junker, Vivien}, + journal={EUR. J. BIOCHEM}, + volume={147}, + pages={9--15}, + year={1985}, + url={http://www.ebi.ac.uk/ena/} +} + +@article{sugawara2008ddbj, + title={DDBJ with new system and face}, + author={Sugawara, Hideaki and Ogasawara, Osamu and Okubo, Kousaku and Gojobori, Takashi and Tateno, Yoshio}, + journal={Nucleic acids research}, + volume={36}, + number={suppl 1}, + pages={D22--D24}, + year={2008}, + publisher={Oxford Univ Press} +} + +@article{chapman2000biopython, + title={Biopython: Python tools for computational biology}, + author={Chapman, Brad and Chang, Jeffrey}, + journal={ACM SIGBIO Newsletter}, + volume={20}, + number={2}, + pages={15--19}, + year={2000}, + publisher={ACM} +} + @incollection{FI09, year={2009}, isbn={978-3-642-04743-5}, @@ -68,6 +165,14 @@ author={Tannier, Eric}, pages={1-12} } +@article{gansner2002drawing, + title={Drawing graphs with dot}, + author={Gansner, Emden and Koutsofios, Eleftherios and North, Stephen}, + journal={Retrieved June}, + volume={13}, + pages={2005}, + year={2002} +} @article{10.1371/journal.pone.0052841, author = {Blouin, Yann AND Hauck, Yolande AND Soler, Charles AND Fabre, Michel AND Vong, Rithy AND Dehan, Céline AND Cazajous, Géraldine AND Massoure, Pierre-Laurent AND Kraemer, Philippe AND Jenkins, Akinbowale AND Garnotel, Eric AND Pourcel, Christine AND Vergnaud, Gilles}, @@ -79,10 +184,23 @@ pages={1-12} volume = {7}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0052841}, pages = {e52841}, - abstract = {Molecular and phylogeographic studies have led to the definition within the
Environmental shotgun sequencing promises to reveal novel and fundamental insights into the hidden world of microbes, but the complexity of analysis required to realize this potential poses unique interdisciplinary challenges.
- }, - number = {3}, - doi = {10.1371/journal.pbio.0050082} -} -@Article{RDogma, -AUTHOR = {Stacia K. Wyman, Robert K. Jansen and Jeffrey L. Boore}, -TITLE = {Automatic annotation of organellar genomes -with DOGMA}, -JOURNAL = {BIOINFORMATICS, oxford Press}, -VOLUME = {20}, -YEAR = {2004}, -NUMBER = {172004}, -PAGES = {3252-3255}, -URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004.pdf}, + +@article{guindon2005phyml, + title={PHYML Onlineâa web server for fast maximum likelihood-based phylogenetic inference}, + author={Guindon, Stephane and Lethiec, Franck and Duroux, Patrice and Gascuel, Olivier}, + journal={Nucleic acids research}, + volume={33}, + number={suppl 2}, + pages={W557--W559}, + year={2005}, + publisher={Oxford Univ Press} +} + +@article{goloboff2008tnt, + title={TNT, a free program for phylogenetic analysis}, + author={Goloboff, Pablo A and Farris, James S and Nixon, Kevin C}, + journal={Cladistics}, + volume={24}, + number={5}, + pages={774--786}, + year={2008}, + publisher={Wiley Online Library} } + +@article{stamatakis2008raxml, + title={The RAxML 7.0. 4 Manual}, + author={Stamatakis, Alexandros}, + journal={Department of Computer Science. Ludwig-Maximilians-Universit{\"a}t M{\"u}nchen}, + year={2008} +} +@article{stamatakis2005raxml, + title={RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees}, + author={Stamatakis, Alexandros and Ludwig, Thomas and Meier, Harald}, + journal={Bioinformatics}, + volume={21}, + number={4}, + pages={456--463}, + year={2005}, + publisher={Oxford Univ Press} +} + + @article{Bakke2009, author = {Bakke, Peter AND Carney, Nick AND DeLoache, Will AND Gearing, Mary AND Ingvorsen, Kjeld AND Lotz, Matt AND McNair, Jay AND Penumetcha, Pallavi AND Simpson, Samantha AND Voss, Laura AND Win, Max AND Heyer, Laurie J. AND Campbell, A. Malcolm}, journal = {PLoS ONE}, @@ -132,9 +264,23 @@ URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004 volume = {4}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0006291}, pages = {e6291}, - abstract = { -Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon