Integrated database of representative Korean history research centers.
Chloroplast-derived sequences were identified by comparing the Vigna mitochondrial genome to a database of representative seed plant chloroplast genomes with BLASTN, and non-coding mitochondrial-like sequences were identified by searching the Vigna genome against a database of all fully sequenced seed plant mitochondrial genomes.
Such a database of representative sequences was used to align closely related streptococcal species to identify specific positions in the 16S rRNA gene for the purpose of species-specific identification.
3PFDB: Database of best-representative; PSSM: Profiles of Protein families; BRP: Best Representative; PSSM: profile of a protein family; FASSM: Function Association using Sequence and Structural Motifs; HMM: Hidden Markov Model; PSI-BLAST: Position Specific Iterative - BLAST.
To facilitate reliable comparisons of rice QTLs, we extracted QTL information from published research papers and constructed a database of 1,051 representative QTLs, which we classified into 21 trait categories.
The computed target PCAIN scores were then correlated with the PCAIN scores (from the seed database) of every representative homologous superfamily member of the identified fold family in order to compute the optimal template, based on similarities at the level of evolutionary origin and function.
The data mining approach is applied to Pfam version 22 and a new database of Best-Representative PSSM profiles (BRPs) of protein families called 3PFDB is developed.
Data were extracted from Macro International Demographic and Health Surveys (DHS) (ICF International, 2013), a database of nationally representative household surveys conducted in low and middle-income countries.
Availability of an approach to identify BRPs and a curated database of best representative PSI-BLAST derived PSSMs for 91.4% of current Pfam family will be a useful resource for the community to perform detailed and specific analysis using family-specific, best-representative PSSM profiles.
The updated database of PFAM family representatives covers 13 672 families from PFAM v 26 (3), and for 13 519 (∼99%) families, the representatives have more than 90% coverage.
To address the issues of redundancy we had used CD-HIT [ 29], a program that removes redundant sequences and generate a database of only the representatives.
