Literature DB >> 12824406

Bioverse: Functional, structural and contextual annotation of proteins and proteomes.

Jason McDermott1, Ram Samudrala.   

Abstract

Functional annotation is routinely performed for large-scale genomics projects and databases. Researchers working on more specific problems, for instance on an individual pathway or complex, also need to be able to quickly, completely and accurately annotate sequences. The Bioverse sequence annotation server (http://bioverse.compbio.washington.edu) provides a web-based interface to allow users to submit protein sequences to the Bioverse framework. Sequences are functionally and structurally annotated and potential contextual annotations are provided. Researchers can also submit candidate genomes for annotation of all proteins encoded by the genome (proteome).

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Year:  2003        PMID: 12824406      PMCID: PMC168957          DOI: 10.1093/nar/gkg550

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  16 in total

1.  InterPro--an integrated documentation resource for protein families, domains and functional sites.

Authors:  R Apweiler; T K Attwood; A Bairoch; A Bateman; E Birney; M Biswas; P Bucher; L Cerutti; F Corpet; M D Croning; R Durbin; L Falquet; W Fleischmann; J Gouzy; H Hermjakob; N Hulo; I Jonassen; D Kahn; A Kanapin; Y Karavidopoulou; R Lopez; B Marx; N J Mulder; T M Oinn; M Pagni; F Servant; C J Sigrist; E M Zdobnov
Journal:  Bioinformatics       Date:  2000-12       Impact factor: 6.937

2.  Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies.

Authors:  Masami Ikeda; Masafumi Arai; Demelo M Lao; Toshio Shimizu
Journal:  In Silico Biol       Date:  2002

3.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

4.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

5.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.

Authors:  Ioannis Xenarios; Lukasz Salwínski; Xiaoqun Joyce Duan; Patrick Higney; Sul-Min Kim; David Eisenberg
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  Recent improvements to the SMART domain-based sequence annotation resource.

Authors:  Ivica Letunic; Leo Goodstadt; Nicholas J Dickens; Tobias Doerks; Joerg Schultz; Richard Mott; Francesca Ciccarelli; Richard R Copley; Chris P Ponting; Peer Bork
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

7.  The PROSITE database, its status in 1999.

Authors:  K Hofmann; P Bucher; L Falquet; A Bairoch
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

8.  PRINTS prepares for the new millennium.

Authors:  T K Attwood; D R Flower; A P Lewis; J E Mabey; S R Morgan; P Scordis; J N Selley; W Wright
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

9.  The ProDom database of protein domain families.

Authors:  F Corpet; J Gouzy; D Kahn
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

10.  A comprehensive analysis of 40 blind protein structure predictions.

Authors:  Ram Samudrala; Michael Levitt
Journal:  BMC Struct Biol       Date:  2002-08-01
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  12 in total

1.  Origin and evolution of new exons in rodents.

Authors:  Wen Wang; Hongkun Zheng; Shuang Yang; Haijing Yu; Jun Li; Huifeng Jiang; Jianning Su; Lei Yang; Jianguo Zhang; Jason McDermott; Ram Samudrala; Jian Wang; Huanming Yang; Jun Yu; Karsten Kristiansen; Gane Ka-Shu Wong; Jun Wang
Journal:  Genome Res       Date:  2005-08-18       Impact factor: 9.043

2.  Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Authors:  Takeshi Itoh; Tsuyoshi Tanaka; Roberto A Barrero; Chisato Yamasaki; Yasuyuki Fujii; Phillip B Hilton; Baltazar A Antonio; Hideo Aono; Rolf Apweiler; Richard Bruskiewich; Thomas Bureau; Frances Burr; Antonio Costa de Oliveira; Galina Fuks; Takuya Habara; Georg Haberer; Bin Han; Erimi Harada; Aiko T Hiraki; Hirohiko Hirochika; Douglas Hoen; Hiroki Hokari; Satomi Hosokawa; Yue-ie Hsing; Hiroshi Ikawa; Kazuho Ikeo; Tadashi Imanishi; Yukiyo Ito; Pankaj Jaiswal; Masako Kanno; Yoshihiro Kawahara; Toshiyuki Kawamura; Hiroaki Kawashima; Jitendra P Khurana; Shoshi Kikuchi; Setsuko Komatsu; Kanako O Koyanagi; Hiromi Kubooka; Damien Lieberherr; Yao-Cheng Lin; David Lonsdale; Takashi Matsumoto; Akihiro Matsuya; W Richard McCombie; Joachim Messing; Akio Miyao; Nicola Mulder; Yoshiaki Nagamura; Jongmin Nam; Nobukazu Namiki; Hisataka Numa; Shin Nurimoto; Claire O'Donovan; Hajime Ohyanagi; Toshihisa Okido; Satoshi Oota; Naoki Osato; Lance E Palmer; Francis Quetier; Saurabh Raghuvanshi; Naomi Saichi; Hiroaki Sakai; Yasumichi Sakai; Katsumi Sakata; Tetsuya Sakurai; Fumihiko Sato; Yoshiharu Sato; Heiko Schoof; Motoaki Seki; Michie Shibata; Yuji Shimizu; Kazuo Shinozaki; Yuji Shinso; Nagendra K Singh; Brian Smith-White; Jun-ichi Takeda; Motohiko Tanino; Tatiana Tatusova; Supat Thongjuea; Fusano Todokoro; Mika Tsugane; Akhilesh K Tyagi; Apichart Vanavichit; Aihui Wang; Rod A Wing; Kaori Yamaguchi; Mayu Yamamoto; Naoyuki Yamamoto; Yeisoo Yu; Hao Zhang; Qiang Zhao; Kenichi Higo; Benjamin Burr; Takashi Gojobori; Takuji Sasaki
Journal:  Genome Res       Date:  2007-01-08       Impact factor: 9.043

3.  The enzymatic and metabolic capabilities of early life.

Authors:  Aaron David Goldman; John A Baross; Ram Samudrala
Journal:  PLoS One       Date:  2012-09-10       Impact factor: 3.240

Review 4.  Cataloging the relationships between proteins: a review of interaction databases.

Authors:  Carol Rohl; Yancey Price; Tiffany B Fischer; Melissa Paczkowski; Michael F Zettel; Jerry Tsai
Journal:  Mol Biotechnol       Date:  2006-09       Impact factor: 2.860

5.  ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

Authors:  Geoffrey Fucile; David Di Biase; Hardeep Nahal; Garon La; Shokoufeh Khodabandeh; Yani Chen; Kante Easley; Dinesh Christendat; Lawrence Kelley; Nicholas J Provart
Journal:  PLoS One       Date:  2011-01-10       Impact factor: 3.240

6.  2DCSi: identification of protein secondary structure and redox state using 2D cluster analysis of NMR chemical shifts.

Authors:  Ching-Cheng Wang; Jui-Hung Chen; Wen-Chung Lai; Woei-Jer Chuang
Journal:  J Biomol NMR       Date:  2007-02-27       Impact factor: 2.582

7.  BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes.

Authors:  Jason McDermott; Michal Guerquin; Zach Frazier; Aaron N Chang; Ram Samudrala
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

8.  VIRGO: computational prediction of gene functions.

Authors:  Naveed Massjouni; Corban G Rivera; T M Murali
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

9.  The Genomes of Oryza sativa: a history of duplications.

Authors:  Jun Yu; Jun Wang; Wei Lin; Songgang Li; Heng Li; Jun Zhou; Peixiang Ni; Wei Dong; Songnian Hu; Changqing Zeng; Jianguo Zhang; Yong Zhang; Ruiqiang Li; Zuyuan Xu; Shengting Li; Xianran Li; Hongkun Zheng; Lijuan Cong; Liang Lin; Jianning Yin; Jianing Geng; Guangyuan Li; Jianping Shi; Juan Liu; Hong Lv; Jun Li; Jing Wang; Yajun Deng; Longhua Ran; Xiaoli Shi; Xiyin Wang; Qingfa Wu; Changfeng Li; Xiaoyu Ren; Jingqiang Wang; Xiaoling Wang; Dawei Li; Dongyuan Liu; Xiaowei Zhang; Zhendong Ji; Wenming Zhao; Yongqiao Sun; Zhenpeng Zhang; Jingyue Bao; Yujun Han; Lingli Dong; Jia Ji; Peng Chen; Shuming Wu; Jinsong Liu; Ying Xiao; Dongbo Bu; Jianlong Tan; Li Yang; Chen Ye; Jingfen Zhang; Jingyi Xu; Yan Zhou; Yingpu Yu; Bing Zhang; Shulin Zhuang; Haibin Wei; Bin Liu; Meng Lei; Hong Yu; Yuanzhe Li; Hao Xu; Shulin Wei; Ximiao He; Lijun Fang; Zengjin Zhang; Yunze Zhang; Xiangang Huang; Zhixi Su; Wei Tong; Jinhong Li; Zongzhong Tong; Shuangli Li; Jia Ye; Lishun Wang; Lin Fang; Tingting Lei; Chen Chen; Huan Chen; Zhao Xu; Haihong Li; Haiyan Huang; Feng Zhang; Huayong Xu; Na Li; Caifeng Zhao; Shuting Li; Lijun Dong; Yanqing Huang; Long Li; Yan Xi; Qiuhui Qi; Wenjie Li; Bo Zhang; Wei Hu; Yanling Zhang; Xiangjun Tian; Yongzhi Jiao; Xiaohu Liang; Jiao Jin; Lei Gao; Weimou Zheng; Bailin Hao; Siqi Liu; Wen Wang; Longping Yuan; Mengliang Cao; Jason McDermott; Ram Samudrala; Jian Wang; Gane Ka-Shu Wong; Huanming Yang
Journal:  PLoS Biol       Date:  2005-02-01       Impact factor: 8.029

10.  INTEGRATOR: interactive graphical search of large protein interactomes over the Web.

Authors:  Aaron N Chang; Jason McDermott; Zachary Frazier; Michal Guerquin; Ram Samudrala
Journal:  BMC Bioinformatics       Date:  2006-03-16       Impact factor: 3.169

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