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PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands.

Yoon SH, Park YK, Kim JF - Nucleic Acids Res. (2014)

Bottom Line: Pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants.With an improved detection scheme, 2673 prokaryotic genomes were analyzed to locate candidate PAIs and REIs.With additional quantitative and qualitative advancements in database content and detection accuracy, PAIDB will continue to facilitate pathogenomic studies of both pathogenic and non-pathogenic organisms.

View Article: PubMed Central - PubMed

Affiliation: Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea Bio-Medical Science Co., Ltd., Daejeon 305-301, Republic of Korea moncher@kribb.re.kr.

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Screenshots of new functional features in PAIDB v2.0. (A) Pages for REIs: 1. a list of REIs; 2. information on the clicked REI; 3. information on the clicked gene; 4. homologs of the selected gene in known virulence genes from PAIDB and VFDB, and known resistance genes from PAIDB, CARD and BacMet. (B) Circular map showing candidate regions of a selected genome. (C) Text and BLAST searches: 5. users can select a database in which to search their text or sequence input; 6. homologs in the BLAST results table are linked to their detailed information (2 and 3). Items clicked on each page that generated the next page are marked in red circles.
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Figure 4: Screenshots of new functional features in PAIDB v2.0. (A) Pages for REIs: 1. a list of REIs; 2. information on the clicked REI; 3. information on the clicked gene; 4. homologs of the selected gene in known virulence genes from PAIDB and VFDB, and known resistance genes from PAIDB, CARD and BacMet. (B) Circular map showing candidate regions of a selected genome. (C) Text and BLAST searches: 5. users can select a database in which to search their text or sequence input; 6. homologs in the BLAST results table are linked to their detailed information (2 and 3). Items clicked on each page that generated the next page are marked in red circles.

Mentions: PAIDB is freely accessible at http://www.paidb.re.kr. The web-based database was redesigned to offer a user-friendly graphic interface with clear visualization of PAIs, REIs and candidate regions in bacterial genomes. The organization of the website follows the previous version of PAIDB (15). The web pages were modified to reflect the new addition of REI data and to accommodate the significantly expanded content (Figure 4A). The menus ‘PAIs’ and ‘REIs’ enable users to casually explore annotated information on each of PAIs and REIs. The ‘Genomes’ menu provides a list of candidate regions of PAIs and REIs in each microbial genome. When a genome accession number is clicked, the ‘Genome Information’ page shows a circular genome map and tables for PAIs, cPAIs, nPAIs, REIs, cREIs and nREIs (Figure 4B). The circular genome map is clickable and links to a linear genome browser view of the selected genomic region. Each of the candidate regions in table format is linked to the feature table, which contains the genes and virulence/resistance determinants.


PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands.

Yoon SH, Park YK, Kim JF - Nucleic Acids Res. (2014)

Screenshots of new functional features in PAIDB v2.0. (A) Pages for REIs: 1. a list of REIs; 2. information on the clicked REI; 3. information on the clicked gene; 4. homologs of the selected gene in known virulence genes from PAIDB and VFDB, and known resistance genes from PAIDB, CARD and BacMet. (B) Circular map showing candidate regions of a selected genome. (C) Text and BLAST searches: 5. users can select a database in which to search their text or sequence input; 6. homologs in the BLAST results table are linked to their detailed information (2 and 3). Items clicked on each page that generated the next page are marked in red circles.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4384037&req=5

Figure 4: Screenshots of new functional features in PAIDB v2.0. (A) Pages for REIs: 1. a list of REIs; 2. information on the clicked REI; 3. information on the clicked gene; 4. homologs of the selected gene in known virulence genes from PAIDB and VFDB, and known resistance genes from PAIDB, CARD and BacMet. (B) Circular map showing candidate regions of a selected genome. (C) Text and BLAST searches: 5. users can select a database in which to search their text or sequence input; 6. homologs in the BLAST results table are linked to their detailed information (2 and 3). Items clicked on each page that generated the next page are marked in red circles.
Mentions: PAIDB is freely accessible at http://www.paidb.re.kr. The web-based database was redesigned to offer a user-friendly graphic interface with clear visualization of PAIs, REIs and candidate regions in bacterial genomes. The organization of the website follows the previous version of PAIDB (15). The web pages were modified to reflect the new addition of REI data and to accommodate the significantly expanded content (Figure 4A). The menus ‘PAIs’ and ‘REIs’ enable users to casually explore annotated information on each of PAIs and REIs. The ‘Genomes’ menu provides a list of candidate regions of PAIs and REIs in each microbial genome. When a genome accession number is clicked, the ‘Genome Information’ page shows a circular genome map and tables for PAIs, cPAIs, nPAIs, REIs, cREIs and nREIs (Figure 4B). The circular genome map is clickable and links to a linear genome browser view of the selected genomic region. Each of the candidate regions in table format is linked to the feature table, which contains the genes and virulence/resistance determinants.

Bottom Line: Pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants.With an improved detection scheme, 2673 prokaryotic genomes were analyzed to locate candidate PAIs and REIs.With additional quantitative and qualitative advancements in database content and detection accuracy, PAIDB will continue to facilitate pathogenomic studies of both pathogenic and non-pathogenic organisms.

View Article: PubMed Central - PubMed

Affiliation: Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea Bio-Medical Science Co., Ltd., Daejeon 305-301, Republic of Korea moncher@kribb.re.kr.

Show MeSH
Related in: MedlinePlus