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A Science Experiment: part 1 - Bert Hubert's writings
a day ago
- The author describes the emotional rollercoaster of potentially discovering something new in biology, including fear of being wrong or scooped.
- DNA replication is a directional process, leading to Okazaki fragments on the lagging strand, which causes asymmetric mutation rates.
- This asymmetry results in GC skew—a measurable excess of G over C on one half of bacterial chromosomes—visible as strikingly straight lines across thousands of genomes.
- The author is analyzing ~23,000 bacterial chromosomes to uncover patterns in GC skew, with plans to share findings in part 2 of the series.
A Science Experiment: part 2 - Bert Hubert's writings
a day ago
- Created and released SkewDB, the largest comprehensive database of GC/TA skews in 25,000 bacterial chromosomes.
- Open-sourced the software that processes 120GB of public NCBI data to generate the database.
- Provided a Jupyter notebook for easy exploration and plotting of the dataset.
- Discovered a method to predict GC/TA skew in Firmicute bacteria, potentially resolving existing debates.
- Identified dozens of bacteria with unexplained asymmetries, including strands with no GC skew and uneven strand sizes.
- Acknowledged the importance of open data sharing and plans to publish a preprint for peer review.
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.
SkewDB - Bert Hubert's writings
a day ago
- SkewDB is a free database containing GC and other skew data for over 53,000 chromosomes and plasmids, last updated on July 5, 2024, now including homopolymer counts and codon bias data.
- The database is created using open-source Antonie software, based on public DNA sequence, annotation, and taxonomic data from NCBI, and provides individual files with 4096-nucleotide granularity for each chromosome.
- Key features include fields for skew gradients (e.g., GC, TA, strand bias), codon position analysis, taxonomic classification, and fit quality metrics, with the project aiming to support research on GC skew and chromosome behavior.

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gc skew

A Science Experiment: part 1 - Bert Hubert's writings

A Science Experiment: part 2 - Bert Hubert's writings

SkewDB: an open database of GC and other microbial skews - Bert Hubert's writings

SkewDB - Bert Hubert's writings