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 | Contains all groups of duplicates (expansions) found found. Each record represents a node in the expansion graph, created by combining local and (or) global matches. |
| Expansions_full | Includes expansions formed by full-mode events only. |
| Expansions_full_tandem | Represents pairs of consecutive full events within an expansion, indicating whether they are in tandem or not. |
| Expansions_transcript_interdependence | Classifies transcript interdependence for each expansion in the Expansions_full table. |
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 | This table is a filtered version of Local_matches, containing only non-reciprocal and reconciled matches identified in the BLAST local search. These matches meet the search criteria, including query coverage, in-frame alignment, and significant non-overlapping. |
| 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 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¶
