Output Description¶
Main file: <output_prefix>_results.db¶
This is the main output database created by exonize.
Main tables¶
If you are only interested in the final results, these are the tables you want to look at:
| Table | Description |
|---|---|
| Expansions | Each record represents a node in an expansion graph, created by combining local and (or) global matches. |
| Expansions_full | Reduced version of Expansions_full containing only expansion graphs constructed from full-length matches. |
| Expansions_full_tandem | Arranges the nodes of expansions in Expansions_full,in consecutive pairs, indicating whether they are in tandem. |
| Expansions_transcript_interdependence | Transcript interdependence classifications for expansions in Expansions_full. |
Other tables¶
If you want to analyze the matches directly, these tables contain the raw data:
| Table | Description |
|---|---|
| Genes | Lists all protein-coding genes analyzed for exon duplications. |
| Local_matches | Contains all matches found by querying representative exons against the genes within which they are situated. These are raw, unfiltered matches found using BLAST. |
| Local_matches_non_reciprocal | Filtered version of Local_matches, containing only non-reciprocal and reconciled matches identified in the local search. These matches meet the query coverage, in-frame alignment, and significant non-overlapping search criteria. |
| Global_matches_non_reciprocal | Contains all matches identified by aligning pairs of representative exons using MUSCLE. All matches meet the peptide identity and fraction of aligned position criteria. |
Note: Combining the
Local_matches_non_reciprocalandGlobal_matches_non_reciprocaltables provides a complete list of all matches identified byexonize. When full-length matches are detected by both methods, they are retained only in theGlobal_matches_non_reciprocaltable and omitted from theLocal_matches_non_reciprocaltable.
Additional files¶
csvs.tar.gz(optional): compressed directory in .tar.gz format, containing individual files in CSV format for each table in the SQLite database, excluding theLocal_matchesandGenestables.<output_prefix>.log: Search settings.
Database structure¶
