Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology

BMC Bioinformatics

Table 15 Classification datasets

	Original (unfiltered) data
			Statistical Properties
Repair pathway	GO ID	No.Sequences	Ave. Length	Median Length	Std. Dev
Base excision repair	0006284	2624	276	251	134.7
DNA dealkylation	0006307	25	203	174	106.8
DNA synthesis during DNA repair	0000731	28	996	1103	581.5
Double-strand break repair	0006302	364	616	609	306.4
Error-prone DNA repair	0045020	46	1075	1077	46.8
Mismatch repair	0006298	1777	617	653	317.3
Nucleotide-excision repair	0006289	2106	732	685	261.6
Postreplication repair	0006301	28	449	350	350.7
Regulation of DNA repair	0006282	264	211	172	161.6
Single strand break repair	0000012	40	476	614	297.8
Other pathways	N/A	45	592	373	486.9
Total		7347	515	415	321.2
	Maximum 90% similarity
			Statistical Properties
Repair pathway	No.Sequences		Ave. Length	Median Length	Std. Dev
Base excision repair		1721	284	260	135.9
Double-strand break repair		266	603	611	309.8
Error-prone DNA repair		36	1077	1082	51.4
Mismatch repair		1020	710	768	274.9
Nucleotide-excision repair		1325	737	689	268.9
Regulation of DNA repair		174	205	168	153.4
Single strand break repair		25	490	403	316.9
Other pathways		78	579.8	373	539.1
Total		4645	534	516	322.7
	Maximum 50% similarity
			Statistical Properties
Repair pathway		No.Sequences	Ave. Length	Median Length	Std. Dev
Base excision repair		630	321	278	185.7
Double-strand break repair		174	656	655	343.6
Mismatch repair		468	718	710	302.6
Nucleotide-excision repair		363	684	633	360.6
Regulation of DNA repair		114	213	168	185.5
Other pathways		81	659	582	496.2
Total		1830	535	434	349.8

The number of proteins extracted from the UniProt database for each of the DNA repair pathways used in classification experiments is shown along with statistical properties regarding seqeuence lengths. Only the types of repair pathways which had sufficient data (minimum 25 proteins) for experiments are shown, along with a combined dataset of the types which did not have enough data.

ISSN: 1471-2105