alanlorenzetti/halo_nr_tx

Halobacterium salinarum NRC-1 non-redundant transcriptome

Generating a non-redundant transcriptome for Halobacterium salinarum

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:

Lorenzetti, A.P.R., Kusebauch, U., Zaramela, L.S., Wu, W-J., de Almeida, J.P.P., Turkarslan, S., de Lomana, A.L.G., Gomes-Filho, J.V., Vêncio, R.Z.N., Moritz, R.L., Koide, T., and Baliga, N.S. (2023). A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon. mSystems, e00816-22.