TAGOPSIN: collating taxa-specific gene and protein functional and structural information

BMC Bioinformatics

Table 1 Case study of the performance of TAGOPSIN

Query	H. sapiens	A. thaliana	S. cerevisiae	E. coli	Streptococcus	Human coronavirus	Human papillomavirus
No of organisms
From Taxonomy	7	5	351	3 365	5 039	27	259
From Nucleotide	0	0	0	1 142	637	2	33
No of curated genomes/chromosomes	24	5	16	1 274	796	4	65
No of CDSs	112 702	48 147	5 989	6 066 761	1 540 276	30	442
No of proteins	17 261	15 383	5 876	17 777	9 037	21	127
No of protein isoforms	16 007	2 196	29	6	0	0	0
No of GO terms	17 597	6 825	6 023	2 614	815	47	54
No of protein domain families	6 108	3 125	3 222	2 281	819	36	12
No of protein 3D structures	39 885	1 472	4 565	1 893	232	27	36
Approx. runtime (hours)	147.83	5.31	3.03	72.35	19.52	3.01	3.18

The statistics of the datasets built for Homo sapiens, Escherichia coli and five other organisms, as indicated, is classified by entity type. Estimated runtimes are on a 64-bit Linux Ubuntu system with 4.7 GiB of RAM and an Intel\(^{\circledR }\) Core^TM i7-6500U CPU @ 2.50 GHz processor. Actual runtimes may vary depending on Internet bandwidth, volume of data to process, and hardware specifications. Here an average bandwidth of 1.1 MB/s was used. The times indicated for H. sapiens and E. coli include time to download and decompress standard data files (updated July/August 2020)

ISSN: 1471-2105