Literature DB >> 33289898

NCBI Genome Workbench: Desktop Software for Comparative Genomics, Visualization, and GenBank Data Submission.

Anatoliy Kuznetsov1, Colleen J Bollin2.   

Abstract

The book chapter introduces the National Center for Biotechnology Information (NCBI) Genome Workbench, a desktop GUI software package to manipulate and visualize complex molecular biology models provided in many data formats. Genome Workbench integrates graphical views and computational tools in a single package to facilitate discoveries. In this chapter we provide a step-by-step protocol guidance on how to do comparative analysis of sequences using NCBI BLAST and multiple sequence alignment algorithms, build phylogenetic trees, and use graphical views for sequences, alignments, and trees to validate the findings. The software package can be used to prepare high-quality whole genome submissions to NCBI. The software package is user-friendly and includes validation and editing tools to fix errors as part of preparing the submission.

Keywords:  Alignment; Analysis; BLAST; Bioinformatics; Clustal; GenBank; Genome; MAFFT; MUSCLE; Phylogenetic; PubMed; Visualization

Mesh：

Year:  2021        PMID： 33289898     DOI： 10.1007/978-1-0716-1036-7_16

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  9 in total

1.  Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.

Authors:  Richard Desper; Olivier Gascuel
Journal:  J Comput Biol       Date:  2002       Impact factor: 1.479

2.  Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting.

Authors:  Richard Desper; Olivier Gascuel
Journal:  Mol Biol Evol       Date:  2003-12-23       Impact factor: 16.240

3.  Plague in small mammals and humans in Rangoon, Burma.

Authors:  J E Brooks; U H Naing; D W Walton; D S Myint; U M Tun; U Thaung; D O Kyi
Journal:  Southeast Asian J Trop Med Public Health       Date:  1977-09       Impact factor: 0.267

4.  Skeletal change in response to altered strain environments: is woven bone a response to elevated strain?

Authors:  D B Burr; M B Schaffler; K H Yang; M Lukoschek; N Sivaneri; J D Blaha; E L Radin
Journal:  Bone       Date:  1989       Impact factor: 4.398

5.  [Cortical electrostimulation in skull and brain injury].

Authors:  F A Gurchin; S V Medvedev; V Iu Puzenko
Journal:  Fiziol Cheloveka       Date:  1988 Mar-Apr

6.  Urinary MHPG: improved tricyclic antidepressant drug selection in clinical practice.

Authors: 
Journal:  Med J Aust       Date:  1979-09-08       Impact factor: 7.738

7.  Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI.

Authors:  Stacy Ciufo; Sivakumar Kannan; Shobha Sharma; Azat Badretdin; Karen Clark; Seán Turner; Slava Brover; Conrad L Schoch; Avi Kimchi; Michael DiCuccio
Journal:  Int J Syst Evol Microbiol       Date:  2018-05-24       Impact factor: 2.747

8.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

Authors:  Nuala A O'Leary; Mathew W Wright; J Rodney Brister; Stacy Ciufo; Diana Haddad; Rich McVeigh; Bhanu Rajput; Barbara Robbertse; Brian Smith-White; Danso Ako-Adjei; Alexander Astashyn; Azat Badretdin; Yiming Bao; Olga Blinkova; Vyacheslav Brover; Vyacheslav Chetvernin; Jinna Choi; Eric Cox; Olga Ermolaeva; Catherine M Farrell; Tamara Goldfarb; Tripti Gupta; Daniel Haft; Eneida Hatcher; Wratko Hlavina; Vinita S Joardar; Vamsi K Kodali; Wenjun Li; Donna Maglott; Patrick Masterson; Kelly M McGarvey; Michael R Murphy; Kathleen O'Neill; Shashikant Pujar; Sanjida H Rangwala; Daniel Rausch; Lillian D Riddick; Conrad Schoch; Andrei Shkeda; Susan S Storz; Hanzhen Sun; Francoise Thibaud-Nissen; Igor Tolstoy; Raymond E Tully; Anjana R Vatsan; Craig Wallin; David Webb; Wendy Wu; Melissa J Landrum; Avi Kimchi; Tatiana Tatusova; Michael DiCuccio; Paul Kitts; Terence D Murphy; Kim D Pruitt
Journal:  Nucleic Acids Res       Date:  2015-11-08       Impact factor: 16.971

9.  GenBank.

Authors:  Eric W Sayers; Mark Cavanaugh; Karen Clark; James Ostell; Kim D Pruitt; Ilene Karsch-Mizrachi
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971
  9 in total
  13 in total

1.  Platelet proteome reveals features of cell death, antiviral response and viral replication in covid-19.

Authors:  Monique R O Trugilho; Isaclaudia G Azevedo-Quintanilha; João S M Gesto; Emilly Caroline S Moraes; Samuel C Mandacaru; Mariana M Campos; Douglas M Oliveira; Suelen S G Dias; Viviane A Bastos; Marlon D M Santos; Paulo C Carvalho; Richard H Valente; Eugenio D Hottz; Fernando A Bozza; Thiago Moreno L Souza; Jonas Perales; Patrícia T Bozza
Journal:  Cell Death Discov       Date:  2022-07-16

2.  Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV).

Authors:  Sanjida H Rangwala; Anatoliy Kuznetsov; Victor Ananiev; Andrea Asztalos; Evgeny Borodin; Vladislav Evgeniev; Victor Joukov; Vadim Lotov; Ravinder Pannu; Dmitry Rudnev; Andrew Shkeda; Eric M Weitz; Valerie A Schneider
Journal:  Genome Res       Date:  2020-11-25       Impact factor: 9.043

3.  Digenic heterozygous mutations of KCNH2 and SCN5A induced young and early-onset long QT syndrome and sinoatrial node dysfunction.

Authors:  Zhe Yang; Yuting Ma; Jiana Huang; Jianzhong Xian; Yin Huang; Linbo Wu; WenLiang Zhu; Feng Wang; Liang Chen; Xiufang Lin; Yubi Lin
Journal:  Ann Noninvasive Electrocardiol       Date:  2021-11-09       Impact factor: 1.468

4.  RGEN-seq for highly sensitive amplification-free screen of off-target sites of gene editors.

Authors:  Alexander Kuzin; Brendan Redler; Jaya Onuska; Alexei Slesarev
Journal:  Sci Rep       Date:  2021-12-08       Impact factor: 4.379

5.  Molecular characterization and phylogenetic studies of Echinococcus granulosus and Taenia multiceps coenurus cysts in slaughtered sheep in Saudi Arabia.

Authors:  Jamila S Al Malki; Nahed Ahmed Hussien
Journal:  Open Life Sci       Date:  2021-11-27       Impact factor: 0.938

6.  Inter-species interactions alter antibiotic efficacy in bacterial communities.

Authors:  Michael J Bottery; Jessica L Matthews; A Jamie Wood; Helle Krogh Johansen; Jon W Pitchford; Ville-Petri Friman
Journal:  ISME J       Date:  2021-10-09       Impact factor: 10.302

7.  In vivo growth of Staphylococcus lugdunensis is facilitated by the concerted function of heme and non-heme iron acquisition mechanisms.

Authors:  Ronald S Flannagan; Jeremy R Brozyna; Brijesh Kumar; Lea A Adolf; Jeffrey John Power; Simon Heilbronner; David E Heinrichs
Journal:  J Biol Chem       Date:  2022-03-10       Impact factor: 5.486

8.  Molecular characterization of matrix metalloproteinase gene family across primates.

Authors:  Yinglian Pan; Yadan Fan; Yanda Lu; Siyuan Peng; Haixue Lin; Qingchun Deng
Journal:  Aging (Albany NY)       Date:  2022-04-20       Impact factor: 5.682

9.  Molecular characterization of Trypanosoma evansi, T. vivax and T. congolense in camels (Camelus dromedarius) of KSA.

Authors:  Jamila S Al Malki; Nahed Ahmed Hussien
Journal:  BMC Vet Res       Date:  2022-01-18       Impact factor: 2.741

10.  Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes.

Authors:  Tatiana G Senkevich; Natalya Yutin; Yuri I Wolf; Eugene V Koonin; Bernard Moss
Journal:  mBio       Date:  2021-07-13       Impact factor: 7.867
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.