Some of Halobacterium salinarum NRC-1 genes are repeated. Reducing it to a non-redundant set of genes can help simplifying analyses. Moreover, there have been several annotation efforts, causing a lot of pain to integrate findings from distinct studies due to non-standardized locus tags.
This is an attempt to create a non-redundant (pseudo)transcriptome for Halobacterium salinarum NRC-1 using as source the annotation released by Pfeiffer et al. 2019. A dictionary containing alternative locus_tag was also created using annotation provided by NCBI's RefSeq prokaryotic automatic annotation pipeline and a custom in-house file derived from the original annotation provided by Ng et al. 2000.
Briefly:
1.1) Pfeiffer et al. 2019 third party annotation was manually downloaded from:
- https://www.ncbi.nlm.nih.gov/nuccore/BK010829 (data/chr.gff3);
- https://www.ncbi.nlm.nih.gov/nuccore/BK010830 (data/pnrc100.gff3);
- https://www.ncbi.nlm.nih.gov/nuccore/BK010831 (data/pnrc200.gff3).
1.2) Files were renamed and concatenated;
1.3) Accession names where replaced in GFF3 file to match those of NCBI RefSeq;
2.1) NCBI RefSeq annotations and genomes (ASM680v1 and ASM6902v1) were automatically downloaded and minimally parsed from the ftp resource;
3.1) Ng et al. 2000 derived annotation containing protein sequences was loaded and parsed;
4.1) For CDS, nucleotide sequences were obtained using the genome and both annotations, and converted to amino acid using the translation table #11. The aa sequences were further clustered using CD-HIT (95% identity) to obtain the non-redundant set;
4.2) For RNAs, nucleotide sequences were obtained using the genome and both annotations. The nt sequences were further clustered using CD-HIT (99% identity) to obtain the non-redundant set;
4.3) A cluster of a single locus_tag, coming from NCBI will be automatically discarded;
5.1) Finally, it is going to knit a Rmd file containing the dictionary table;
Please, check the final report here.
If you use the content of this repository, please, reference the following study: