Kahn D

References (6)

Title : Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype - Jaillon_2004_Nature_431_946
Author(s) : Jaillon O , Aury JM , Brunet F , Petit JL , Stange-Thomann N , Mauceli E , Bouneau L , Fischer C , Ozouf-Costaz C , Bernot A , Nicaud S , Jaffe D , Fisher S , Lutfalla G , Dossat C , Segurens B , Dasilva C , Salanoubat M , Levy M , Boudet N , Castellano S , Anthouard V , Jubin C , Castelli V , Katinka M , Vacherie B , Biemont C , Skalli Z , Cattolico L , Poulain J , de Berardinis V , Cruaud C , Duprat S , Brottier P , Coutanceau JP , Gouzy J , Parra G , Lardier G , Chapple C , McKernan KJ , McEwan P , Bosak S , Kellis M , Volff JN , Guigo R , Zody MC , Mesirov J , Lindblad-Toh K , Birren B , Nusbaum C , Kahn D , Robinson-Rechavi M , Laudet V , Schachter V , Quetier F , Saurin W , Scarpelli C , Wincker P , Lander ES , Weissenbach J , Roest Crollius H
Ref : Nature , 431 :946 , 2004
Abstract : Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
ESTHER : Jaillon_2004_Nature_431_946
PubMedSearch : Jaillon_2004_Nature_431_946
PubMedID: 15496914
Gene_locus related to this paper: tetng-3neur , tetng-4neur , tetng-ACHE , tetng-BCHE , tetng-h3cfz4 , tetng-h3ci57 , tetng-h3cl30 , tetng-h3cnh2 , tetng-nlgn2b , tetng-h3czr1 , tetng-h3dbr5 , tetng-nlgn2a , tetng-nlgn3b , tetng-q4ref8 , tetng-q4rjp3 , tetng-q4rjy3 , tetng-q4rk53 , tetng-q4rk63 , tetng-q4rk66 , tetng-q4rkk3 , tetng-q4rli3 , tetng-q4rn09 , tetng-q4rqj4 , tetng-q4rqz6 , tetng-q4rr22 , tetng-q4rru9 , tetng-q4rtq6 , tetng-q4rvf8 , tetng-q4rwa0 , tetng-q4rx90 , tetng-q4ryv8 , tetng-q4ryz3 , tetng-q4s0h8 , tetng-q4s5x0 , tetng-q4s6r1 , tetng-q4s6t6 , tetng-q4s7e3 , tetng-q4s7x6 , tetng-q4s8t5 , tetng-q4s9w9 , tetng-q4s050 , tetng-q4s091 , tetng-q4s144 , tetng-q4s309 , tetng-q4s578 , tetng-q4sal4 , tetng-q4sbm6 , tetng-q4sbp0 , tetng-q4sbu0 , tetng-q4sd49 , tetng-q4ser6 , tetng-q4sfm7 , tetng-q4sgm5 , tetng-q4sgv2 , tetng-q4sh74 , tetng-q4shl7 , tetng-q4si60 , tetng-q4sie5 , tetng-q4sku6 , tetng-q4smu0 , tetng-q4smy3 , tetng-q4snp0 , tetng-q4snq3 , tetng-q4spa7 , tetng-q4spq0 , tetng-q4sqr3 , tetng-q4sty0 , tetng-q4suu2 , tetng-q4suz1 , tetng-q4sxh3 , tetng-q4syn6 , tetng-q4szk0 , tetng-q4szy0 , tetng-q4t3m9 , tetng-q4t4a1 , tetng-q4t6m1 , tetng-q4t7r6 , tetng-q4t173 , tetng-q4t826 , tetng-q4t920 , tetng-q4ta33 , tetng-q4tab8 , tetng-q4tb62 , tetng-q4tbe2 , tetng-h3dbw2 , tetng-h3cpc8 , tetng-h3cjy0 , tetng-h3d966 , tetng-h3d3e3 , tetng-h3d961 , tetng-h3ctg6 , tetng-h3dde8 , tetng-h3dde9 , tetng-h3det9 , tetng-h3cre8 , tetng-h3dfb4 , tetng-h3clj8

Title : The composite genome of the legume symbiont Sinorhizobium meliloti - Galibert_2001_Science_293_668
Author(s) : Galibert F , Finan TM , Long SR , Puhler A , Abola P , Ampe F , Barloy-Hubler F , Barnett MJ , Becker A , Boistard P , Bothe G , Boutry M , Bowser L , Buhrmester J , Cadieu E , Capela D , Chain P , Cowie A , Davis RW , Dreano S , Federspiel NA , Fisher RF , Gloux S , Godrie T , Goffeau A , Golding B , Gouzy J , Gurjal M , Hernandez-Lucas I , Hong A , Huizar L , Hyman RW , Jones T , Kahn D , Kahn ML , Kalman S , Keating DH , Kiss E , Komp C , Lelaure V , Masuy D , Palm C , Peck MC , Pohl TM , Portetelle D , Purnelle B , Ramsperger U , Surzycki R , Thebault P , Vandenbol M , Vorholter FJ , Weidner S , Wells DH , Wong K , Yeh KC , Batut J
Ref : Science , 293 :668 , 2001
Abstract : The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.
ESTHER : Galibert_2001_Science_293_668
PubMedSearch : Galibert_2001_Science_293_668
PubMedID: 11474104
Gene_locus related to this paper: rhime-PTRB , rhime-R01391 , rhime-R01762 , rhime-R02260 , rhime-RB0025 , rhime-RB0171

Title : Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid - Barnett_2001_Proc.Natl.Acad.Sci.U.S.A_98_9883
Author(s) : Barnett MJ , Fisher RF , Jones T , Komp C , Abola AP , Barloy-Hubler F , Bowser L , Capela D , Galibert F , Gouzy J , Gurjal M , Hong A , Huizar L , Hyman RW , Kahn D , Kahn ML , Kalman S , Keating DH , Palm C , Peck MC , Surzycki R , Wells DH , Yeh KC , Davis RW , Federspiel NA , Long SR
Ref : Proc Natl Acad Sci U S A , 98 :9883 , 2001
Abstract : The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be specifically involved in symbiosis, pSymA contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.
ESTHER : Barnett_2001_Proc.Natl.Acad.Sci.U.S.A_98_9883
PubMedSearch : Barnett_2001_Proc.Natl.Acad.Sci.U.S.A_98_9883
PubMedID: 11481432
Gene_locus related to this paper: rhime-RA0091 , rhime-RA0138 , rhime-RA0313 , rhime-RA0428 , rhime-RA0633 , rhime-RA0724 , rhime-RA0950 , rhime-RA0980 , rhime-RA1008 , rhime-RA1044 , rhime-RA1075 , rhime-RA1107

Title : The InterPro database, an integrated documentation resource for protein families, domains and functional sites - Apweiler_2001_Nucleic.Acids.Res_29_37
Author(s) : Apweiler R , Attwood TK , Bairoch A , Bateman A , Birney E , Biswas M , Bucher P , Cerutti L , Corpet F , Croning MD , Durbin R , Falquet L , Fleischmann W , Gouzy J , Hermjakob H , Hulo N , Jonassen I , Kahn D , Kanapin A , Karavidopoulou Y , Lopez R , Marx B , Mulder NJ , Oinn TM , Pagni M , Servant F , Sigrist CJ , Zdobnov EM
Ref : Nucleic Acids Research , 29 :37 , 2001
Abstract : Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http:\/\/www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.
ESTHER : Apweiler_2001_Nucleic.Acids.Res_29_37
PubMedSearch : Apweiler_2001_Nucleic.Acids.Res_29_37
PubMedID: 11125043

Title : Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021 - Capela_2001_Proc.Natl.Acad.Sci.U.S.A_98_9877
Author(s) : Capela D , Barloy-Hubler F , Gouzy J , Bothe G , Ampe F , Batut J , Boistard P , Becker A , Boutry M , Cadieu E , Dreano S , Gloux S , Godrie T , Goffeau A , Kahn D , Kiss E , Lelaure V , Masuy D , Pohl T , Portetelle D , Puhler A , Purnelle B , Ramsperger U , Renard C , Thebault P , Vandenbol M , Weidner S , Galibert F
Ref : Proc Natl Acad Sci U S A , 98 :9877 , 2001
Abstract : Sinorhizobium meliloti is an alpha-proteobacterium that forms agronomically important N(2)-fixing root nodules in legumes. We report here the complete sequence of the largest constituent of its genome, a 62.7% GC-rich 3,654,135-bp circular chromosome. Annotation allowed assignment of a function to 59% of the 3,341 predicted protein-coding ORFs, the rest exhibiting partial, weak, or no similarity with any known sequence. Unexpectedly, the level of reiteration within this replicon is low, with only two genes duplicated with more than 90% nucleotide sequence identity, transposon elements accounting for 2.2% of the sequence, and a few hundred short repeated palindromic motifs (RIME1, RIME2, and C) widespread over the chromosome. Three regions with a significantly lower GC content are most likely of external origin. Detailed annotation revealed that this replicon contains all housekeeping genes except two essential genes that are located on pSymB. Amino acid/peptide transport and degradation and sugar metabolism appear as two major features of the S. meliloti chromosome. The presence in this replicon of a large number of nucleotide cyclases with a peculiar structure, as well as of genes homologous to virulence determinants of animal and plant pathogens, opens perspectives in the study of this bacterium both as a free-living soil microorganism and as a plant symbiont.
ESTHER : Capela_2001_Proc.Natl.Acad.Sci.U.S.A_98_9877
PubMedSearch : Capela_2001_Proc.Natl.Acad.Sci.U.S.A_98_9877
PubMedID: 11481430
Gene_locus related to this paper: rhime-ACVB , rhime-PIP1 , rhime-PIP2 , rhime-PIP3 , rhime-PLDB , rhime-PTRB , rhime-q92ju9 , rhime-q92ke0 , rhime-q92nd1 , rhime-q92td3 , rhime-R00281 , rhime-R00428 , rhime-R00762 , rhime-R01391 , rhime-R01482 , rhime-R01647 , rhime-R01737 , rhime-R01762 , rhime-R01861 , rhime-R01962 , rhime-R01994 , rhime-R02203 , rhime-R02260 , rhime-R02262 , rhime-R02478 , rhime-R02490 , rhime-R02995 , rhime-R03193 , sinmb-a0a0e0ub90

Title : Browsing protein families via the 'Rich Family Description' format - Corpet_1999_Bioinformatics_15_1020
Author(s) : Corpet F , Gouzy J , Kahn D
Ref : Bioinformatics , 15 :1020 , 1999
Abstract : MOTIVATION: Multiple alignments of protein sequences are the basis of structural and functional analysis of protein families. It is however difficult even for an expert biologist to comprehend an alignment of more than 50 to 100 homologous sequences.
RESULTS: This paper presents a browser for the analysis of multiple alignments of large numbers of protein sequences. Phylogenetic trees and consensus sequences are computed and used to summarise the alignments; these data are stored in a structure called Rich Family Description. Summary alignments and trees are displayed in HTML pages and can be developed or reduced by the user. This browser is used to display the ProDom domain families on the Web. Its zooming facilities allow extracting information from alignments of more than 1000 homologous sequences.
ESTHER : Corpet_1999_Bioinformatics_15_1020
PubMedSearch : Corpet_1999_Bioinformatics_15_1020
PubMedID: 10745992