< 3^rd term

Nucleotide database

Last update on the 21^st of October, 2017

In this task we study several nucleotide databases of NCBI and capabilities they provide.

Brief description of tasks

The following tasks were done and reported via Google Forms:

• quallity assession of Zea mays genome assembly;
• 7 keys used in feature tables were described;
• Global Ocean Sampling Expedition project description;
• mitochondrial genomes of Paramecium caudatum were found and counted.

Some tasks needed additional information, which is stored in this page.

Mitochondrial proteins of P. caudatum

protein_genes.ods

P. caudatum (fig. 1) is one of the most recognizable species in Ciliophora taxon. To investigate its mitochondrion genome a query (paramecium caudatum[Organism]) AND gene_in_mitochondrion[PROP] and "complete genome"[KYWD] was submitted into NCBI databases. Two entries were found, a RefSeq database one under accession NC_014262 was taken for futher investigation. The table with genomic organisation of mitochondrial proteins is available in protein_genes.ods file.

Several species were studied for whole mitochondrial genomes. Search results and processed data is shown in table 1. Mitochondrion genome size and number of its genes are correlated so does MTgenome and genome size. Interestingly, genome size grows faster then MTgenome one, which stands for uncommon functions of mitochondria and nuclei in cell life.

Genome sizes

To estimate typical genome sizes of life kingdoms the NCBI Genome database was used. Obtained data was proccessed through LibreOffice Calc and results were merged into table 2. Median size is proposed as typical for the corresponding group of organisms.