Mysql dump of curated pfam28 domains used for similarity search evaluation
This repository contains the Mysql database tables used to support the analyses published in Pearson, Li, and Lopez (2016) Nuc. Acids Res. "Query-seeded iterative sequence similarity searching improves selectivity 5–20-fold" doi: 10.1093/nar/gkw1207 PDF.
The database consists of five tables taken from Pfam (pfam.xfam.org) release 27, and another 3 tables that describe the subset of pfam domains that met the RPD3 criteria of model-length and phylogenetic diversity.
| table | origin/description |
|---|---|
| RPD3_domain_xref | auto_pfamA_reg_full for the 339 RPD3 domains/clans in RPD3 sequences |
| RPD3_pfamA | the domain/clan relationships for the pfamA domains in RPD3 |
| RPD3_pfamA_joined_split | not used |
| clan | pfam27 (clans for all RPD3 domains) |
| clan_membership | pfam27 |
| pfamA | pfam27 (all RPD3 domains contained in RPD3 sequences) |
| pfamA_reg_full_significant | pfam27 (domain annotations for RPD3 sequences) |
| pfamseq | pfam27 (RPD3 selected sequences) |
| pfamseq | pfam27 (RPD3 selected sequences) |
Because of file size constraints,the pfamseq table must be loaded from multiple files. The table can first be created using pfamseq.sql, and then populated using the commands:
mysql -h host -u user RPD3 < pfamseq.sql
load data local infile "pfamseq.txt.part_aa" into table pfamseq;
load data local infile "pfamseq.txt.part_ab" into table pfamseq;
load data local infile "pfamseq.txt.part_ac" into table pfamseq;