+@article{Sayers01012011,
+author = {Sayers \emph{et al}},
+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{SMMR+13,
title={Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis},
url={http://www.nature.com/ng/journal/v45/n2/full/ng.2517.html},
DOI={10.1089/cmb.2010.0092}
}
+@article{Eisen2007,
+ author = {Eisen, Jonathan A},
+ journal = {PLoS Biol},
+ publisher = {Public Library of Science},
+ title = {Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes},
+ year = {2007},
+ month = {03},
+ volume = {5},
+ url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050082},
+ pages = {e82},
+ abstract = {
+ <p>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.</p>
+ },
+ number = {3},
+ doi = {10.1371/journal.pbio.0050082}
+}
+
+@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},
+ journal={Bioinformatics},
+ volume={23},
+ number={9},
+ pages={1061--1067},
+ year={2007},
+ publisher={Oxford Univ Press}
+}
+
+@article{parra2000geneid,
+ title={Geneid in drosophila},
+ author={Parra, Gen{\'\i}s and Blanco, Enrique and Guig{\'o}, Roderic},
+ journal={Genome research},
+ volume={10},
+ number={4},
+ pages={511--515},
+ year={2000},
+ publisher={Cold Spring Harbor Lab}
+}
+
+@article{birney2004genewise,
+ title={GeneWise and genomewise},
+ author={Birney, Ewan and Clamp, Michele and Durbin, Richard},
+ journal={Genome research},
+ volume={14},
+ number={5},
+ pages={988--995},
+ 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 O’Donovan, 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},
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},
volume = {7},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0052841},
pages = {e52841},
- abstract = {<p>Molecular and phylogeographic studies have led to the definition within the <italic>Mycobacterium tuberculosis</italic> complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major <italic>M. tuberculosis</italic> lineages were identified, with only two <italic>M. africanum</italic> and one <italic>M. bovis</italic> isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.</p>},
number = {12},
doi = {10.1371/journal.pone.0052841}
}
+
+
+
+@article{zafar2002coregenes,
+ title={CoreGenes: A computational tool for identifying and cataloging},
+ author={Zafar, Nikhat and Mazumder, Raja and Seto, Donald},
+ journal={BMC bioinformatics},
+ volume={3},
+ number={1},
+ pages={12},
+ year={2002},
+ publisher={BioMed Central Ltd}
+}
+
@Article{17623808,
AUTHOR = {Gomez-Valero, Laura and Rocha, Eduardo P C and Latorre, Amparo and Silva, Francisco J},
TITLE = {Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction.},
PubMedID = {17623808},
ISSN = {1088-9051}
}
-@article{Eisen2007,
- author = {Eisen, Jonathan A},
- journal = {PLoS Biol},
- publisher = {Public Library of Science},
- title = {Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes},
- year = {2007},
- month = {03},
- volume = {5},
- url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050082},
- pages = {e82},
- abstract = {
- <p>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.</p>
- },
- 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 Online—a 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},
volume = {4},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0006291},
pages = {e6291},
- abstract = {
-<p>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 <italic>Halorhabdus utahensis</italic> to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus ribosome-binding site. Additionally, we conducted laboratory experiments to test <italic>H. utahensis</italic> growth and enzyme activity. Current annotation practices need to improve in order to more accurately reflect a genome's biological potential. We make specific recommendations that could improve the quality of microbial annotation projects.</p>
-},
number = {7},
doi = {10.1371/journal.pone.0006291}
}
+
+@article{altschul1990basic,
+ title={Basic local alignment search tool},
+ author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
+ journal={Journal of molecular biology},
+ volume={215},
+ number={3},
+ pages={403--410},
+ year={1990},
+ publisher={Elsevier}
+}
+
+@article{geneVision,
+ title={DNASTAR- GenVision Software for Genomic Visualizations},
+ author={DNASTAR},
+ url = {http://www.dnastar.com/products/genvision.php}
+}
+
+@article{mcfadden2001primary,
+ title={Primary and secondary endosymbiosis and the origin of plastids},
+ author={McFadden, Geoffrey Ian},
+ journal={Journal of Phycology},
+ volume={37},
+ number={6},
+ pages={951--959},
+ year={2001},
+ publisher={Wiley Online Library}
+}
+
+@article{li2013complete,
+ title={Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)},
+ author={Li, Xi and Zhang, Ti-Cao and Qiao, Qin and Ren, Zhumei and Zhao, Jiayuan and Yonezawa, Takahiro and Hasegawa, Masami and Crabbe, M James C and Li, Jianqiang and Zhong, Yang},
+ journal={PloS one},
+ volume={8},
+ number={3},
+ pages={e58747},
+ year={2013},
+ publisher={Public Library of Science}
+}
