Sars-Cov-2 and Mers sequences from human host with no unknown characters
Data files
Jan 02, 2024 version files 25.61 MB
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Mers_dataset.txt
6.60 KB
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README.md
2.60 KB
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Sars_Cov_2_dataset_restricted.txt
149.45 KB
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Sars_Cov_2_dataset.txt
25.45 MB
Abstract
The datasets are organized as follows: first column, number of bases in a given sequence; second, third, fourth and fifth columns, number of bases of type A, C, G and T, respectively, in the same sequence.
1) Sars-Cov-2 dataset. This dataset contains number of bases for the complete genome sequences from a human host, with none unknown characters. In the NCBI database, there are about 950.000 sequences with these characteristics.
2) Restricted Sars-Cov-2 dataset: This dataset contains number of bases for the complete sequences from a human host, with no unknown characters, with 29903 bases, that is of the same length as the reference sequence NC045512.2. We obtained, from the NCBI database, about 5600 sequences with such features.
3) Mers dataset: This dataset contains number of bases for the complete sequences of about 200 complete genome sequences from a human host, with no unknown characters.
README: Sars-Cov-2 and Mers sequences from human host with none unknown characters
https://doi.org/10.5061/dryad.9s4mw6mp2
We uploaded three datasets organized as follows: first column, number of bases in a given sequence; second, third, fourth and fifth columns, number of bases of type A, C, G and T, respectively, in the same sequence.
1) Sars-Cov-2 dataset. This dataset contains number of bases for the complete genome sequences from a human host, with none unknown characters. In the NCBI database, there are about 950.000 sequences with these characteristics.
2) Restricted Sars-Cov-2 dataset: This dataset contains number of bases for the complete sequences from a human host, with no unknown characters, with 29903 bases, that is of the same length as the reference sequence NC045512.2. We obtained, from the NCBI database, about 5800 sequences with such features.
3) Mers dataset: This dataset contains number of bases for the complete sequences of about 250 complete genome sequences from a human host, with no unknown characters.
Description of the data
Each dataset is organized as follows: first column, number of bases in a given sequence; second, third, fourth and fifth columns, number of bases of type A, C, G and T, respectively, in the same sequence. Each row reports the data calculated for successive sequences following the same order of the raw data (see links below).
Sharing information
Raw data are freely available at the following address:
Code
Readfasta: a C++ code for sequence base count. Datasets are obtained We provide a C++ computer code that reads a dataset of nucleic acid sequences in FASTA format and returns the number of bases in each sequence. The output file seqcount.txt contains a table organized as follows: first column, number of bases in a given sequence; second, third, fourth and fifth columns, number of bases of type A, C, G and T, respectively, in the same sequence. Each row reports the data calculated for successive sequences following the same order of the dataset.
Methods
Raw datasets are genome sequences retrieved from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov). The sequences were filtered according to the following criteria:
1) Sars-Cov-2 dataset. This dataset contains complete genome sequences from a human host, with none unknown characters. In the NCBI database, there are about 950.000 sequences with these characteristics.
2) Restricted Sars-Cov-2 dataset: This dataset contains complete genome sequences from a human host, with no unknown characters, with 29903 bases, that is of the same length as the reference sequence NC045512.2. We obtained, from the NCBI database, about 5600 sequences with such features.
3) Mers dataset: We selected about 200 complete genome sequences from a human host, with no unknown characters.
Raw data have been processed through a C++ code (provided with the datsets) that reads a dataset of nucleic acid sequences in FASTA format and returns the number of bases in each sequence. The output file seqcount.txt contains a table organized as follows: first column, number of bases in a given sequence; second, third, fourth and fifth columns, number of bases of type A, C, G and T, respectively, in the same sequence. Each row reports the data calculated for successive sequences following the same order of the raw datasets.