SkewDB: an open database of GC and other microbial skews - Bert Hubert's writings
a day ago
- SkewDB is an open, downloadable database of GC skew and a dozen other skews for all 28,000 bacterial chromosomes from NCBI.
- The database is created using the open-source Antonie DNA software and includes an online viewer with graphs.
- GC skew refers to the tendency of leading replication strands to have excess G nucleotides and lagging strands excess C, first described in 1996 but not fully explained.
- The database can help generate and falsify hypotheses, detect mis-assembled or multi-chromosome genomes, and reveal unusual patterns like asymmetric GC skew.
- Notable observations include asymmetric GC skew in some bacteria, the strand bias hypothesis linking gene orientation to skew, and large discrepancies in leading/lagging strand lengths.
- SkewDB also provides various sub-skews (e.g., within genes, codon positions) and strand bias data, summarized per chromosome and on a 4096-nucleotide basis.