X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/chloroplast13.git/blobdiff_plain/fb06fc26916e64c8e6c452ee7424b6433e255f0f..124dccf169638e62feadd4095293eef191a0f3c6:/biblio.bib diff --git a/biblio.bib b/biblio.bib index 2a4eade..d5aaff6 100644 --- a/biblio.bib +++ b/biblio.bib @@ -21,6 +21,50 @@ pages={1097--1112}, DOI={10.1089/cmb.2010.0092} } +@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{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}, @@ -36,6 +80,14 @@ 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}, @@ -51,6 +103,32 @@ pages={1-12} number = {12}, doi = {10.1371/journal.pone.0052841} } + +@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}, +abstract ={In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.}, +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{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.}, @@ -62,4 +140,104 @@ PAGES = {1178-85}, URL = {http://www.biomedsearch.com/nih/Reconstructing-ancestor-Mycobacterium-leprae-dynamics/17623808.html}, 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 = { +

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 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}, + publisher = {Public Library of Science}, + title = {Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis}, + year = {2009}, + month = {07}, + 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 Halorhabdus utahensis 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 H. utahensis 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.

+}, + 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} } \ No newline at end of file