Literature DB >> 12952886

GANESH: software for customized annotation of genome regions.

Derek Huntley1, Holger Hummerich, Damian Smedley, Sasivimol Kittivoravitkul, Mark McCarthy, Peter Little, Marek Sergot.   

Abstract

GANESH is a software package designed to support the genetic analysis of regions of human and other genomes. It provides a set of components that may be assembled to construct a self-updating database of DNA sequence, mapping data, and annotations of possible genome features. Once one or more remote sources of data for the target region have been identified, all sequences for that region are downloaded, assimilated, and subjected to a (configurable) set of standard database-searching and genome-analysis packages. The results are stored in compressed form in a relational database, and are updated automatically on a regular schedule so that they are always immediately available in their most up-to-date versions. A Java front-end, executed as a stand alone application or web applet, provides a graphical interface for navigating the database and for viewing the annotations. There are facilities for importing and exporting data in the format of the Distributed Annotation System (DAS), enabling a GANESH database to be used as a component of a DAS configuration. The system has been used to construct databases for about a dozen regions of human chromosomes and for three regions of mouse chromosomes.

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Year:  2003        PMID： 12952886      PMCID： PMC403729          DOI： 10.1101/gr.698103

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  18 in total

1.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

2.  Experimental annotation of the human genome using microarray technology.

Authors:  D D Shoemaker; E E Schadt; C D Armour; Y D He; P Garrett-Engele; P D McDonagh; P M Loerch; A Leonardson; P Y Lum; G Cavet; L F Wu; S J Altschuler; S Edwards; J King; J S Tsang; G Schimmack; J M Schelter; J Koch; M Ziman; M J Marton; B Li; P Cundiff; T Ward; J Castle; M Krolewski; M R Meyer; M Mao; J Burchard; M J Kidd; H Dai; J W Phillips; P S Linsley; R Stoughton; S Scherer; M S Boguski
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

Review 3.  Genome annotation: from sequence to biology.

Authors:  L Stein
Journal:  Nat Rev Genet       Date:  2001-07       Impact factor: 53.242

4.  A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes.

Authors:  J B Hogenesch; K A Ching; S Batalov; A I Su; J R Walker; Y Zhou; S A Kay; P G Schultz; M P Cooke
Journal:  Cell       Date:  2001-08-24       Impact factor: 41.582

5.  The Ensembl genome database project.

Authors:  T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  Assembly of the working draft of the human genome with GigAssembler.

Authors:  W J Kent; D Haussler
Journal:  Genome Res       Date:  2001-09       Impact factor: 9.043

7.  Disperse: a simple and efficient approach to parallel database searching.

Authors:  R Clifford; A J Mackey
Journal:  Bioinformatics       Date:  2000-06       Impact factor: 6.937

8.  A physical map of the human genome.

Authors:  J D McPherson; M Marra; L Hillier; R H Waterston; A Chinwalla; J Wallis; M Sekhon; K Wylie; E R Mardis; R K Wilson; R Fulton; T A Kucaba; C Wagner-McPherson; W B Barbazuk; S G Gregory; S J Humphray; L French; R S Evans; G Bethel; A Whittaker; J L Holden; O T McCann; A Dunham; C Soderlund; C E Scott; D R Bentley; G Schuler; H C Chen; W Jang; E D Green; J R Idol; V V Maduro; K T Montgomery; E Lee; A Miller; S Emerling; R Gibbs; S Scherer; J H Gorrell; E Sodergren; K Clerc-Blankenburg; P Tabor; S Naylor; D Garcia; P J de Jong; J J Catanese; N Nowak; K Osoegawa; S Qin; L Rowen; A Madan; M Dors; L Hood; B Trask; C Friedman; H Massa; V G Cheung; I R Kirsch; T Reid; R Yonescu; J Weissenbach; T Bruls; R Heilig; E Branscomb; A Olsen; N Doggett; J F Cheng; T Hawkins; R M Myers; J Shang; L Ramirez; J Schmutz; O Velasquez; K Dixon; N E Stone; D R Cox; D Haussler; W J Kent; T Furey; S Rogic; S Kennedy; S Jones; A Rosenthal; G Wen; M Schilhabel; G Gloeckner; G Nyakatura; R Siebert; B Schlegelberger; J Korenberg; X N Chen; A Fujiyama; M Hattori; A Toyoda; T Yada; H S Park; Y Sakaki; N Shimizu; S Asakawa; K Kawasaki; T Sasaki; A Shintani; A Shimizu; K Shibuya; J Kudoh; S Minoshima; J Ramser; P Seranski; C Hoff; A Poustka; R Reinhardt; H Lehrach
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

9.  A physical map of 30,000 human genes.

Authors:  P Deloukas; G D Schuler; G Gyapay; E M Beasley; C Soderlund; P Rodriguez-Tomé; L Hui; T C Matise; K B McKusick; J S Beckmann; S Bentolila; M Bihoreau; B B Birren; J Browne; A Butler; A B Castle; N Chiannilkulchai; C Clee; P J Day; A Dehejia; T Dibling; N Drouot; S Duprat; C Fizames; S Fox; S Gelling; L Green; P Harrison; R Hocking; E Holloway; S Hunt; S Keil; P Lijnzaad; C Louis-Dit-Sully; J Ma; A Mendis; J Miller; J Morissette; D Muselet; H C Nusbaum; A Peck; S Rozen; D Simon; D K Slonim; R Staples; L D Stein; E A Stewart; M A Suchard; T Thangarajah; N Vega-Czarny; C Webber; X Wu; J Hudson; C Auffray; N Nomura; J M Sikela; M H Polymeropoulos; M R James; E S Lander; T J Hudson; R M Myers; D R Cox; J Weissenbach; M S Boguski; D R Bentley
Journal:  Science       Date:  1998-10-23       Impact factor: 47.728

10.  The Pfam protein families database.

Authors:  Alex Bateman; Ewan Birney; Lorenzo Cerruti; Richard Durbin; Laurence Etwiller; Sean R Eddy; Sam Griffiths-Jones; Kevin L Howe; Mhairi Marshall; Erik L L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971
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