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CHPVDB--a sequence annotation database for Chandipura virus.

Dikhit MR, Rana SP, Das P, Sahoo GC - Bioinformation (2009)

Bottom Line: As the gap between the amount of sequence information and functional characterization widens, increasing efforts are being directed to the development of databases.CHPVDB is our effort to provide virologist such a one-step information center.For basic curation of protein information, the database relies on features from other selected databases, servers and published reports.

View Article: PubMed Central - PubMed

Affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India - 800007.

ABSTRACT

Unlabelled: Databases containing proteomic information have become indispensable for virology studies. As the gap between the amount of sequence information and functional characterization widens, increasing efforts are being directed to the development of databases. For virologist, it is therefore desirable to have a single data collection point which integrates research related data from different domains. CHPVDB is our effort to provide virologist such a one-step information center. We describe herein the creation of CHPVDB, a new database that integrates information of different proteins in to a single resource. For basic curation of protein information, the database relies on features from other selected databases, servers and published reports. This database facilitates significant relationship between molecular analysis, cleavage sites, possible protein functional families assigned to different proteins of Chandipura virus (CHPV) by SVMProt and related tools.

Availability: The database is freely available at http://chpvdb.biomedinformri.org/.

No MeSH data available.


Related in: MedlinePlus

CHPVDB snapshot. (a) search option; (b) results by protein name; (c) results by protein family; (d) results byNCBI locus ID; (e) results by instability index.
© Copyright Policy - open-access
Related In: Results  -  Collection


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Figure 2: CHPVDB snapshot. (a) search option; (b) results by protein name; (c) results by protein family; (d) results byNCBI locus ID; (e) results by instability index.

Mentions: CHPVDB can be queried to obtain the information about the protein sequences in many ways. Data stored inCHPVDB can be accessed in the following ways: (i)Search by protein name: The user can enter the desiredprotein name to access the Meta information about the protein sequences; (ii) Search by protein functional family:The user can select the different protein functional family to find out the protein functional group of differentstructural and non‐structural proteins; (iii) Search by NCBI locus ID: The user can enter the NCBI locus ID to obtainChandipura virus protein sequence information; (iv) Search by Instability Index: To find out the stable and unstableprotein, user can search by instability index; (v) Compare two proteins: CHPVDB can be queried to obtain theinformation about protein‐protein comparison. The user can enter the corresponding NCBI locus ID or select theprotein name to compare two proteins. Database visualization helps the user to process, interpret and actupon large stored data sets. CHPVDB provides a number of web‐based forms for querying the dataset and selectingeither a more detailed view of molecular annotation, cleavage 5 sites and functional family or for viewing thecomparison between two selected proteins. The overall feature is shown in Figure 2. In an effort to improve accessto diverse CHPV data, The CHPVDB has been modified to include an abundance of linkage to other database including PUBMED [13] for related paper abstracts andNCBI for corresponding sequences.


CHPVDB--a sequence annotation database for Chandipura virus.

Dikhit MR, Rana SP, Das P, Sahoo GC - Bioinformation (2009)

CHPVDB snapshot. (a) search option; (b) results by protein name; (c) results by protein family; (d) results byNCBI locus ID; (e) results by instability index.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2655048&req=5

Figure 2: CHPVDB snapshot. (a) search option; (b) results by protein name; (c) results by protein family; (d) results byNCBI locus ID; (e) results by instability index.
Mentions: CHPVDB can be queried to obtain the information about the protein sequences in many ways. Data stored inCHPVDB can be accessed in the following ways: (i)Search by protein name: The user can enter the desiredprotein name to access the Meta information about the protein sequences; (ii) Search by protein functional family:The user can select the different protein functional family to find out the protein functional group of differentstructural and non‐structural proteins; (iii) Search by NCBI locus ID: The user can enter the NCBI locus ID to obtainChandipura virus protein sequence information; (iv) Search by Instability Index: To find out the stable and unstableprotein, user can search by instability index; (v) Compare two proteins: CHPVDB can be queried to obtain theinformation about protein‐protein comparison. The user can enter the corresponding NCBI locus ID or select theprotein name to compare two proteins. Database visualization helps the user to process, interpret and actupon large stored data sets. CHPVDB provides a number of web‐based forms for querying the dataset and selectingeither a more detailed view of molecular annotation, cleavage 5 sites and functional family or for viewing thecomparison between two selected proteins. The overall feature is shown in Figure 2. In an effort to improve accessto diverse CHPV data, The CHPVDB has been modified to include an abundance of linkage to other database including PUBMED [13] for related paper abstracts andNCBI for corresponding sequences.

Bottom Line: As the gap between the amount of sequence information and functional characterization widens, increasing efforts are being directed to the development of databases.CHPVDB is our effort to provide virologist such a one-step information center.For basic curation of protein information, the database relies on features from other selected databases, servers and published reports.

View Article: PubMed Central - PubMed

Affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India - 800007.

ABSTRACT

Unlabelled: Databases containing proteomic information have become indispensable for virology studies. As the gap between the amount of sequence information and functional characterization widens, increasing efforts are being directed to the development of databases. For virologist, it is therefore desirable to have a single data collection point which integrates research related data from different domains. CHPVDB is our effort to provide virologist such a one-step information center. We describe herein the creation of CHPVDB, a new database that integrates information of different proteins in to a single resource. For basic curation of protein information, the database relies on features from other selected databases, servers and published reports. This database facilitates significant relationship between molecular analysis, cleavage sites, possible protein functional families assigned to different proteins of Chandipura virus (CHPV) by SVMProt and related tools.

Availability: The database is freely available at http://chpvdb.biomedinformri.org/.

No MeSH data available.


Related in: MedlinePlus