Computational cloning of drug target genes of a parasitic nematode, Oesophagostomum dentatum

Romine, Nathan M; Martin, Richard J; Beetham, Jeffrey K

doi:10.1186/1471-2156-14-55

BMC Genomic Data

Table 1 Drug-target genes and high similarity initial-assembly contigs at multiple k-mers

From: Computational cloning of drug target genes of a parasitic nematode, Oesophagostomum dentatum

*C. elegans*Target gene				21-mer HSPs			23-mer HSPs			25-mer HSPs			27-mer HSPs
ID	Acc #		CDS len	#	$\bar{X}$	R	#	$\bar{X}$	R	#	$\bar{X}$	R	#	$\bar{X}$	R
lev-1	CAB03148		1419	3	148	99-219	3	238	174-294	5	238	96-525	4	237	114-381
lev-8	CAB01685		1596	2	147	126-168	1	255	255	1	108	108		nd	nd
unc-29	CAB02308		1482	12	144	105-168	7	259	120-480	8	248	132-426	11	202	96-402
unc-38	CCD69819		1524	6	180	111-294	9	184	90-375	9	283	84-1098	8	339	87-1380
unc-63	CCD66192		1524	3	272	105-576	5	247	96-510	5	263	105-510	5	235	105-510
avr-14	CCD61323		1251	1	90	90	2	112	102-123	2	114	105-123	4	111	105-123
avr-15	CAB03329		1437	4	163	123-210	7	154	123-192	6	140	105-210	3	185	123-240
ben-1	CAB00853		1335	2	163	108-219	1	111	111	1	114	114	3	102	90-117
glc-1	CAB07361		1305	1	123	123	1	108	108	1	318	318	1	237	237
glc-2	CCD62432		1305	4	198	147-318	1	879	879	1	939	939	3	375	207-582
glc-3	CCD69051		1455	3	146	87-207	2	115	111-120	2	102	93-111	4	117	99-144
glc-4	CCD65896		1503	6	192	111-279	2	702	249-1155	2	702	249-1155	2	702	249-1155
	29-mer HSPs			31-mer HSPs			33-mer HSPs			35-mer HSPs			37-mer HSPs
ID	#	$\bar{X}$	R	#	$\bar{X}$	R	#	$\bar{X}$	R	#	$\bar{X}$	R	#	$\bar{X}$	R
lev-1	5	219	93-420	11	150	99-330	9	181	114-255	8	207	102-558	6	334	138-657
lev-8			nd			nd			nd			nd			nd
unc-29	8	223	120-465	9	171	96-378	8	180	96-396	2	172	162-183	4	173	144-207
unc-38	7	493	90-1473	7	416	84-1473	6	472	108-1473	4	708	261-1473	3	890	360-1473
unc-63	3	227	105-297	4	285	105-414	3	275	105-414	1	414	414	2	277	141-414
avr-14	3	123	111-135	5	145	111-207	6	169	123-270	5	202	123-321	5	240	123-327
avr-15	5	156	90-243	7	153	96-291	4	132	93-213	4	138	96-243	4	108	108-111
ben-1	2	97	93-102	4	99	90-120	3	99	96-102	3	109	87-135	5	109	93-129
glc-1	1	237	237			nd	2	141	141-141			nd			nd
glc-2	3	261	147-393	2	439	135-744	2	475	207-744	2	387	171-603	2	336	333-339
glc-3	3	112	111-114	7	169	93-330	7	120	90-168	5	145	117-213	6	153	111-189
glc-4	2	702	249-1155	2	702	249-1155	2	702	249-1155	2	702	249-1155	1	972	972
	39-mer HSPs			41-mer HSPs			43-mer HSPs			45-mer HSPs			47-mer HSPs
ID	#	$\bar{X}$	R	#	$\bar{X}$	R	#	$\bar{X}$	R	#	$\bar{X}$	R	#	$\bar{X}$	R
lev-1	3	564	339-807	1	1392	1392	1	1401	1401	2	619	345-894	3	245	219-270
lev-8			nd			nd			nd			nd			nd
unc-29			nd			nd			nd			nd			nd
unc-38	1	1473	1473	1	1473	1473	2	868	264-1473	1	1473	1473			nd
unc-63			nd			nd			nd			nd			nd
avr-14	1	390	390	1	219	219			nd			nd			nd
avr-15	2	111	111-111				1	120	120	1	174	174	1	174	174
ben-1	7	100	75-120	10	138	90-234	16	115	84-234	25	114	87-348	15	160	90-453
glc-1			nd			nd			nd			nd			nd
glc-2			nd			nd			nd			nd			nd
glc-3	3	618	84-1383			nd	1	378	378			nd			nd
glc-4	1	1428	1428	1	1428	1428	1	972	972	1	972	972	1	1428	1428

C. elegans target genes (name (ID), GenBank accession number (Acc #) and coding sequence length (CDS len)) used to BLASTx-query a database comprised of the initial de novo library assembly. For each k-mer (e.g. “21 mer HSPs”) are listed in columns the number of high scoring pairs identified (HSP; “#”), the mean HSP length in DNA bases (“ $\bar{X}$ ”), and the range of HSP-lengths (“R”) with minimum and maximum length shown. Bold HSP-length values indicates the longest HSP identified among all k-mers for a given target gene. “nd” indicate no high-similarity HSPs were identified at that k-mer.

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