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EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

Ndhlovu A, Durand PM, Hazelhurst S - Database (Oxford) (2015)

Bottom Line: To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled.Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality.EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Medicine Laboratory, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, Sydney Brenner Institute of Molecular Bioscience, The Mount, 9 Jubilee Road, Parktown 2193, Johannesburg, South Africa, andrew.ndhlovu@students.wits.ac.za.

No MeSH data available.


Workflow for the development and compilation of EvoDB.
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bav065-F1: Workflow for the development and compilation of EvoDB.

Mentions: The retrieval of sequences and the determination of the ω maximum-likelihood estimate (MLE) profiles using CODEML are computationally expensive. The computational resources of the Wits Core Cluster (ZA-WITS-CORE) of 13 nodes running Scientific Linux 6.3 were utilized for achieving parallelism. PFAM-A seed alignments and the GenBank database, including the Swiss-Prot and TrEMBL in the Uniprot resource (9) database were made available locally. Resources and scheduling were managed by Maui/PBS and TORQUE systems, respectively. Each PFAM entry was submitted as a job using custom scripts. The compilation pipeline is provided in Figure 1.Figure 1.


EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

Ndhlovu A, Durand PM, Hazelhurst S - Database (Oxford) (2015)

Workflow for the development and compilation of EvoDB.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492416&req=5

bav065-F1: Workflow for the development and compilation of EvoDB.
Mentions: The retrieval of sequences and the determination of the ω maximum-likelihood estimate (MLE) profiles using CODEML are computationally expensive. The computational resources of the Wits Core Cluster (ZA-WITS-CORE) of 13 nodes running Scientific Linux 6.3 were utilized for achieving parallelism. PFAM-A seed alignments and the GenBank database, including the Swiss-Prot and TrEMBL in the Uniprot resource (9) database were made available locally. Resources and scheduling were managed by Maui/PBS and TORQUE systems, respectively. Each PFAM entry was submitted as a job using custom scripts. The compilation pipeline is provided in Figure 1.Figure 1.

Bottom Line: To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled.Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality.EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Medicine Laboratory, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, Sydney Brenner Institute of Molecular Bioscience, The Mount, 9 Jubilee Road, Parktown 2193, Johannesburg, South Africa, andrew.ndhlovu@students.wits.ac.za.

No MeSH data available.