Fungal genome resources at NCBI

References

• Altschul , SF , Gish , W , Miller , W , Myers , EW and Lipman , DJ. 1990 . Basic local alignment search tool . J Mol Biol , 215 : 403 – 410 .
   PubMed Web of Science ®Google Scholar
• Benson , DA , Karsch-Mizrachi , I , Lipman , DJ , Ostell , J and Sayers , EW. 2011 . GenBank . Nucleic Acids Res , 39 ( Database issue ) : D32 – 7 .
   Google Scholar
• Berman , H , Henrick , K , Nakamura , H and Markley , JL . 2007 . The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data . Nucleic Acids Res , 35 ( Database issue ) : D301 – D303 .
   PubMed Web of Science ®Google Scholar
• Bhagwat , AA and Bhagwat , M. 2008 . Methods and tools for comparative genomics of foodborne pathogens . Foodborne Pathog Dis , 5 : 487 – 497 .
   Google Scholar
• Caspi , R , Altman , T , Dale , JM , Dreher , K , Fulcher , CA , Gilham , F , Kaipa , P , Karthikeyan , AS , Kothari , A Krummenacker , M . 2010 . The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases . Nucleic Acids Res , 38 ( Database issue ) : D473 – D479 .
   Google Scholar
• Cochrane , G , Bates , K , Apweiler , R , Tateno , Y , Mashima , J , Kosuge , T , Mizrachi , IK , Schafer , S and Fetchko , M. 2006 . Evidence standards in experimental and inferential INSDC Third Party Annotation data . OMICS , 10 : 105 – 113 .
   Google Scholar
• Cooper , PS , Lipshultz , D , Matten , WT , McGinnis , SD , Pechous , S , Romiti , ML , Tao , T , Valjavec-Gratian , M and Sayers , EW . 2010 . Education resources of the National Center for Biotechnology Information . Brief Bioinform , 11 : 563 – 569 .
   Google Scholar
• Croft , D , O‘Kelly , G , Wu , G , Haw , R , Gillespie , M , Matthews , L , Caudy , M , Garapati , P , Gopinath , G Jassal , B . 2011 . Reactome: a database of reactions, pathways and biological processes . Nucleic Acids Res , 39 ( Database issue ) : D691 – 7 .
   PubMed Web of Science ®Google Scholar
• Finn , RD , Mistry , J , Tate , J , Coggill , P , Heger , A , Pollington , JE , Gavin , OL , Gunesekaran , P , Ceric , G Forslund , K . 2010 . The Pfam protein families database . Nucleic Acids Res , 38 ( Database Issue ) : D211 – 222 .
   Google Scholar
• Geer , LY , Marchler-Bauer , A , Geer , RC , Han , L , He , J , He , S , Liu , C , Shi , W and Bryant , SH. 2010 . The NCBI BioSystems database . Nucleic Acids Res , 38 ( Database issue ) : D492 – D496 .
   Google Scholar
• Hatayama , M and Aruga , J . 2010 . Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions . BMC Evol Biol , 10 : 53
   Google Scholar
• Kaminuma , E , Kosuge , T , Kodama , Y , Aono , H , Mashima , J , Gojobori , T , Sugawara , H , Ogasawara , O , Takagi , T Okubo , K . 2011 . DDBJ progress report . Nucleic Acids Res , 39(Database issue):D22–7
   Google Scholar
• Kanehisa , M , Goto , S , Kawashima Furumichi , M , Tanabe , M and Hirakawa , M. 2010 . KEGG for representation and analysis of molecular networks involving diseases and drugs . Nucleic Acids Res , 38 ( Database issue ) : D355 – D360 .
   PubMed Web of Science ®Google Scholar
• Kapustin , Y , Souvorov , A , Tatusova , T and Lipman , D. 2008 . Splign: algorithms for computing spliced alignments with identification of paralogs . Biol Direct , 3 : 20
   PubMed Web of Science ®Google Scholar
• Kim , KH , Willger , SD , Park , SW , Puttikamonkul , S , Grahl , N , Cho , Y , Mukhopadhyay , B , Cramer , RA Jr and Lawrence , CB. 2009 . TmpL, a transmembrane protein required for intracellular redox homeostasis and virulence in a plant and an animal fungal pathogen . PLoS Pathog , 5 ( 11 ) : e1000653
   Google Scholar
• Klimke , W , Agarwala , R , Badretdin , A , Chetvernin , S , Ciufo , S , Fedorov , B , Kiryutin , B , O‘Neill , K , Resch , W Resenchuk , S . 2009 . The National Center for Biotechnology Information's Protein Clusters Database . Nucleic Acids Res , 37 ( Database issue ) : D216 – 23 .
   Google Scholar
• Leinonen , R , Akhtar , R , Birney , E , Bower , L , Cerdeno-Tárraga , A , Cheng , Y , Cleland , I , Faruque , N , Goodgame , N Gibson , R . 2011a . The European nucleotide archive . Nucleic Acids Res , 39(Database issue):D28–31
   Google Scholar
• Leinonen , R , Sugawara , H and Shumway , M. 2011b . The sequence read archive . Nucleic Acids Res , 39 ( Database issue ) : D19 – 21 .
   PubMed Web of Science ®Google Scholar
• Letunic , I , Doerks , T and Bork , P. 2009 . SMART 6: recent updates and new developments . Nucleic Acids Res , 37 ( Database issue ) : D229 – D232 .
   Google Scholar
• Maglott , D , Ostell , J , Pruitt , KD and Tatusova , T. 2011 . Entrez Gene: gene-centered information at NCBI . Nucleic Acids Res , 39 ( Database issue ) : D52 – 7 .
   Google Scholar
• Marchler-Bauer , A , Lu , S , Anderson , JB , Chitsaz , F , Derbyshire , MK , Deweese-Scott , C , Fong , JH , Geer , LY , Geer , RC Gonzales , NR . 2011 . CDD: a Conserved Domain Database for the functional annotation of proteins . Nucleic Acids Res , 39 ( Database issue ) : D225 – 9 .
   PubMed Web of Science ®Google Scholar
• Papadopoulos , JS and Agarwala , R. 2007 . COBALT: constraint-based alignment tool for multiple protein sequences . Bioinformatics , 23 ( 9 ) : 1073 – 1079 .
   PubMed Web of Science ®Google Scholar
• Pruitt , KD , Tatusova , T , Klimke , W and Maglott , DR. 2009 . NCBI Reference Sequences: current status, policy and new initiatives . Nucleic Acids Res. , 37 ( Database issue ) : D32 – 6 .
   Google Scholar
• Salzberg , SL , Church , D , DiCuccio , M , Yaschenko , E and Ostell , J. 2004 . The genome assembly archive: a new public resource . PLoS Biol , 2 ( 9 ) : e285
   Google Scholar
• Sayers , EW , Barrett , T , Benson , DA , Bolton , E , Bryant , SH , Canese , K , Chetvernin , V , Church , DM , Dicuccio , M Federhen , S . 2011 . Database resources of the National Center for Biotechnology Information . Nucleic Acids Res , 39 ( Database issue ) : D38 – 51 .
   PubMedGoogle Scholar
• Tatusov , RL , Fedorova , ND , Jackson , JD , Jacobs , AR , Kiryutin , B , Koonin , EV , Krylov , DM , Mazumder , R , Mekhedov , SL Nikolskaya , AN . 2003 . The COG database: an updated version includes eukaryotes . BMC Bioinform , 4 : 41
   PubMed Web of Science ®Google Scholar
• The UniProt Consortium . 2011 . Ongoing and future developments at the Universal Protein Resource . Nucleic Acids Res , 39 ( Database issue ) : D214 – 9 .
   Google Scholar