Literature DB >> 12682188

BIBI, a bioinformatics bacterial identification tool.

G Devulder1, G Perrière, F Baty, J P Flandrois.   

Abstract

BIBI was designed to automate DNA sequence analysis for bacterial identification in the clinical field. BIBI relies on the use of BLAST and CLUSTAL W programs applied to different subsets of sequences extracted from GenBank. These sequences are filtered and stored in a new database, which is adapted to bacterial identification.

Mesh：

Year:  2003        PMID： 12682188      PMCID： PMC153906          DOI： 10.1128/JCM.41.4.1785-1787.2003

Source DB:  PubMed          Journal:  J Clin Microbiol        ISSN： 0095-1137            Impact factor:   5.948


  8 in total

Review 1.  Ribosomal DNA sequencing as a tool for identification of bacterial pathogens.

Authors:  C P Kolbert; D H Persing
Journal:  Curr Opin Microbiol       Date:  1999-06       Impact factor: 7.934

2.  ATV: display and manipulation of annotated phylogenetic trees.

Authors:  C M Zmasek; S R Eddy
Journal:  Bioinformatics       Date:  2001-04       Impact factor: 6.937

3.  Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species.

Authors:  C Y Turenne; L Tschetter; J Wolfe; A Kabani
Journal:  J Clin Microbiol       Date:  2001-10       Impact factor: 5.948

4.  DIALIGN: finding local similarities by multiple sequence alignment.

Authors:  B Morgenstern; K Frech; A Dress; T Werner
Journal:  Bioinformatics       Date:  1998       Impact factor: 6.937

5.  WWW-query: an on-line retrieval system for biological sequence banks.

Authors:  G Perrière; M Gouy
Journal:  Biochimie       Date:  1996       Impact factor: 4.079

Review 6.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

7.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors:  J D Thompson; D G Higgins; T J Gibson
Journal:  Nucleic Acids Res       Date:  1994-11-11       Impact factor: 16.971

8.  Database resources of the National Center for Biotechnology Information.

Authors:  D L Wheeler; D M Church; A E Lash; D D Leipe; T L Madden; J U Pontius; G D Schuler; L M Schriml; T A Tatusova; L Wagner; B A Rapp
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971
  8 in total
  52 in total

1.  Evaluation of the GenBank, EzTaxon, and BIBI services for molecular identification of clinical blood culture isolates that were unidentifiable or misidentified by conventional methods.

Authors:  Kyung Sun Park; Chang-Seok Ki; Cheol-In Kang; Yae-Jean Kim; Doo Ryeon Chung; Kyong Ran Peck; Jae-Hoon Song; Nam Yong Lee
Journal:  J Clin Microbiol       Date:  2012-03-07       Impact factor: 5.948

2.  Tuf gene sequence analysis has greater discriminatory power than 16S rRNA sequence analysis in identification of clinical isolates of coagulase-negative staphylococci.

Authors:  Sang Mee Hwang; Myoung Shin Kim; Kyoung Un Park; Junghan Song; Eui-Chong Kim
Journal:  J Clin Microbiol       Date:  2011-10-12       Impact factor: 5.948

3.  First report of Staphylococcal clinical isolates in Mexico with linezolid resistance caused by cfr: evidence of in vivo cfr mobilization.

Authors:  Rodrigo E Mendes; Lalitagauri Deshpande; Eduardo Rodriguez-Noriega; James E Ross; Ronald N Jones; Rayo Morfin-Otero
Journal:  J Clin Microbiol       Date:  2010-06-02       Impact factor: 5.948

4.  Clostridium sordellii brain abscess diagnosed by 16S rRNA gene sequencing.

Authors:  F Valour; S Boisset; L Lebras; B Martha; A Boibieux; T Perpoint; C Chidiac; T Ferry; D Peyramond
Journal:  J Clin Microbiol       Date:  2010-07-07       Impact factor: 5.948

5.  Marine bacteria from Danish coastal waters show antifouling activity against the marine fouling bacterium Pseudoalteromonas sp. strain S91 and zoospores of the green alga Ulva australis independent of bacteriocidal activity.

Authors:  Nete Bernbom; Yoke Yin Ng; Staffan Kjelleberg; Tilmann Harder; Lone Gram
Journal:  Appl Environ Microbiol       Date:  2011-10-14       Impact factor: 4.792

Review 6.  Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases.

Authors:  Jill E Clarridge
Journal:  Clin Microbiol Rev       Date:  2004-10       Impact factor: 26.132

7.  Nocardia ignorata, a new agent of human nocardiosis isolated from respiratory specimens in Europe and soil samples from Kuwait.

Authors:  Verónica Rodríguez-Nava; Andrée Couble; Z U Khan; M Pérouse de Montclos; L Brasme; Cruz Villuendas; Claudie Molinard; Patrick Boiron; Frédéric Laurent
Journal:  J Clin Microbiol       Date:  2005-12       Impact factor: 5.948

8.  Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species.

Authors:  Verónica Rodríguez-Nava; Andrée Couble; Gregory Devulder; Jean-Pierre Flandrois; Patrick Boiron; Frédéric Laurent
Journal:  J Clin Microbiol       Date:  2006-02       Impact factor: 5.948

9.  Tsukamurella tyrosinosolvens--an unusual case report of bacteremic pneumonia after lung transplantation.

Authors:  Armelle Ménard; Sébastien Degrange; Olivia Peuchant; Thi Diem Tien Nguyen; Claire Dromer; Jeanne Maugein
Journal:  Ann Clin Microbiol Antimicrob       Date:  2009-11-12       Impact factor: 3.944

10.  Delineating thermophilic xylanase from Bacillus licheniformis DM5 towards its potential application in xylooligosaccharides production.

Authors:  Arabinda Ghosh; Saikat Sutradhar; Debabrat Baishya
Journal:  World J Microbiol Biotechnol       Date:  2019-01-31       Impact factor: 3.312
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