SQL and Perl scripts to support "Using Relational Databases for Improved Sequence Similarity Searching and Large-Scale Genomic Analyses"
| Programs | description |
|---|---|
load_seqdb_local.pl |
Load a FASTA format sequence database into the seqdb_demo database |
load_taxonomy_local.pl |
load information from the NCBI taxonomy database into seqdb_demo database |
load_search_bl_tab.pl |
load a set of search results in BLAST tabular format into the search_demo database |
| SQL scripts | description |
|---|---|
create_seqdb_demo.sql |
create the seqdb_demo database and assign user permissions |
seqdb_demo.sql |
initialize the tables in seqdb_demo |
load_seqdb_local.sql |
SQL to load PROTEIN.TAB, ANNOT.TAB, and INFO.TAB into seqdb_demo |
qfo_load_accession2taxid.sql |
associate accessions from the qfo_demo database with sequences in seqdb_demo |
load_accession2taxid.sql |
associate accessions from the NCBI nr database with sequences in seqdb_demo |
human_seq.sql |
produce a set of human Uniprot sequences in FASTA format |
mammalia_seq.sql |
produce a set of mammalian Uniprot sequences in FASTA format from seqdb_demo |
mammalia_acc.sql |
produce a set of accessions for mammalian Uniprot sequences from seqdb_demo |
ecoli_seq.sql |
produce a set of E. coli Uniprot sequences in FASTA format |
create_search_demo.sql |
create the search_demo database and assign user permissions |
search_demo.sql |
initialize the tables in search_demo |
ecoli_v_human_shared.sql |
report counts of E. coli sequences in human, and vice-versa, using search_demo |
ecoli_v_human_hits.sql |
report best scores between E. coli and human sequences using search_demo |
ecoli_v_qfo_kingdom.sql |
build a temporary table listing the query_id and kingdom taxon_id |
ecoli_v_qfo_kingdom_summ.sql |
summarize hits between E. coli queries and sequences in qfo_demo |
In addition, the run_seqdb_demo.sh script is provided, which
exercises all the steps outlined in Unit 9.4. However, this script
must be downloaded before the CPBI_seqdb_demo2 package, because it
downloads the package.
William R Pearson [email protected]