Table 2: Analyses of Selected B. malayi L3i EST Sequences

g	Proteins of nematological or immunological interest
	Clone name	dbest accession number	cDNA size (bp)	maximum length (bp)	no. of siblings (SL1)	no. of siblings (conv.)	SL and poly (A)+	short identification
	Housekeeping genes: Ribosomal proteins
a	Large Subunit	(37 clones encoding 19 proteins)
	SW3ICA457	354135	>1200	400	0	1	-,-	ribosomal protein L3
	AS3ISB260	281225	nd	433	1	0	SL, -	ribosomal protein L6
	SW3ICA134	291544	1100	383	0	2	-,-	ribosomal protein L8
	AS3ISB031	217710	nd	329	1	0	SL, -	ribosomal protein L10
	SW3ICA284	291640	600	328	0	1	-,-	ribosomal protein L11
	AS3ISA037	217664	nd	320	1	0	SL, -	ribosomal protein L13a
	SW3ICA024	217726	700	268	0	9	-,-	ribosomal protein L19
	SW3ICA400	343564	600	425	0	1	SL,-	ribosomal protein L23
	AS3ISB013	217685	nd	318	1	0	SL, -	ribosomal protein L26
	AS3ISA007	217662	nd	250	3	0	SL, -	ribosomal protein L30a
	AS3ISA006	216945	500	504	2	1	SL, A+	ribosomal protein L30e
	AS3ISB209	281233	nd	351	1	0	SL, A+	ribosomal protein L31
	AS3ISB169	281211	nd	353	2	0	SL, -	ribosomal protein L32
	AS3ISB300	281209	nd	468	2	0	SL, -	ribosomal protein L35
	AS3ISB063	364462	nd	370	3	0	SL, A+	ribosomal protein L35a (#1)
	AS3ISB326	259983	nd	463	1	0	SL, A+	ribosomal protein L35a (#2)
	AS3ISB011	217686	nd	334	2	0	SL, -	ribosomal protein L36
	AS3ISB347	281851	nd	400	1	0	SL, A+	ribosomal protein L37
	SW3ICA417	354097	400	368	0	1	-,-	ribosomal protein L37a
b	Small Subunit	(30 clones encoding 20 proteins)
	SW3ICA220	291595	1000	267	0	1	-,-	ribosomal protein S2
	SW3ICA018	217587	900	306	0	2	-,-	ribosomal protein S3
	SW3ICA421	354093	1100	513	0	1	-,-	ribosomal protein S4
	SW3ICA292	309252	900	422	0	1	-,-	ribosomal protein S8
	AS3ISB087	364470	500	307	1	1	SL,-	ribosomal protein S12
	AS3ISB267	281841	nd	580	1	2	SL, A+	ribosomal protein S10
	AS3ISA013	217656	nd	50	1	0	SL, -	ribosomal protein S13
	AS3ISB128	364479	nd	474	2	2	SL, -	ribosomal protein S14
	AS3ISA008	217661	nd	350	1	0	SL, -	ribosomal protein S15a
	AS3ISB218	281239	nd	458	1	0	SL,-	ribosomal protein S15
	AS3ISB238	281229	nd	391	1	0	SL, -	ribosomal protein S16
	AS3ISB314	276439	nd	546	1	0	SL, -	ribosomal protein S17
	AS3ISB020	217700	nd	318	1	0	SL, -	ribosomal protein S18
	AS3ISB059	217715	nd	408	1	0	SL, -	ribosomal protein S19
	AS3ISB223	281262	nd	365	1	0	SL, -	ribosomal protein S20/S22
	AS3ISB349	281853	nd	355	1	0	SL, A+	ribosomal protein S21
	SW3ICA324	320165	nd	333	0	1	-,-	ribosomal protein S25
	AS3ISB264	241466	nd	521	2	0	SL, A+	ribosomal protein S26
	AS3ISB131	217794	nd	300	2	1	SL, A+	ribosomal protein S28
	AS3ISB383	281861	nd	399	1	0	SL, A+	ribosomal protein S29
c	Others	(17 clones encoding 4 proteins)
	AS3ISB027	217694	nd	513	10	0	SL, A+	ribosomal protein P1, aka A2
	AS3ISB032	217709	nd	445	1	0	SL, A+	ribosomal protein P2
	SW3ICA366	343525	500	290	0	1	-,-	ribosome binding protein p34 (adenylate cyclase like)
	AS3ISA028	217668	nd	407	4	1	SL, -	ubiquitin-ribosomal protein fusion
d	Housekeeping genes: Structural and muscle proteins
	AS3ISB280	276430	nd	471	2	0	SL,-	histone H2A
	SW3ICA331	320172	nd	364	0	1	-,-	histone H3
	SW3ICA381	343528	>2000	323	0	1	-,-	major body wall myosin heavy chain
	AS3ISA014	217655	600	505	5	2	SL,-	myosin light chain
	SW3ICA109	217607	500	349	0	1	-,-	endosomal protein
	SW3ICA245	291615	2000	323	0	1	-,-	actin-2B
	SW3ICA209	291586	600	320	0	1	-,-	alpha crystallin A chain
	SW3ICA137	291546	500	508	0	4	-,-	microtubule-associated protein 1 light chain 3
	SW3ICA011	217583	2000	310	0	2	-,-	alpha-tubulin
	AS3ISB037	217706	nd	313	1	0	SL,-	calmodulin
	SW3ICA126	291538	500	366	0	1	-,-	C.elegans unc-87 (calponin-like thin filament protein)
	SW3ICA144	291549	2000	354	0	1	-,-	T-complex polypeptide 1 (tcp-1) alpha subunit
	SW3ICA004	217577	1200	340	0	1	-,-	ADP/ATP carrier protein
	SW3ICA339	320180	nd	359	0	1	-,-	Duchenne muscular dystrophy brain product
e	Housekeeping genes: Enzymes
	SW3ICA032	217596	1,300	378	0	1	-,-	triosephosphate isomerase
	SW3ICA258	291647	800	388	0	1	-,-	glyceraldehybe-3-phosphate dehydrogenase
	SW3ICA445	354125	>2000	584	0	1	-,-	malate dehydrogenase, malate oxidoreductase
	SW3ICA132	291543	600	318	0	1	-,-	enolase (2 phosphoglycerate dehydratase)
	SW3ICA112	217610	1,000	377	0	1	-,-	alcohol dehydrogenase (NADP+)
	SW3ICA113	217611	2000	340	0	1	-,-	fatty acid desaturase
	SW3ICA348	320189	1600	379	0	1	-,-	sterol esterase
	SW3ICA448	354128	600	589	0	1	-,-	lactoylglutathione lyase, glyoxalase
	SW3ICA007	217579	1300	428	0	8	-,-	cytochrome C oxidase polypeptide I
	SW3ICA125	291537	2000	341	0	1	-,-	casein kinase I
	AS3ISA028	217713	nd	505	4	0	SL,A+	ubiquitin
	AS3ISA053	217769	nd	150	3	0	SL,-	HMG protein
	AS3ISB030	217711	nd	490	3	0	SL,-	tumour protein
	AS3ISB170	281201	nd	378	1	0	SL,-	RNA polymerase II
	AS3ISA020	217663	nd	575	5	1	SL,A+	nucleoside diphosphate kinase
	AS3ISB256	281238	nd	515	3	0	SL,-	H+-transporting ATP synthase (EC 3.6.1.34) chain f
	SW3ICA253	291643	2500	320	0	1	-,-	vacuolar H+-ATPase 116kDa subunit
	SW3ICA271	291628	1100	384	0	1	-,-	vacuolar ATP synthase 32 kd subunit
	SW3ICA004	217577	1500	287	0	2	-,-	ADP/ATP translocase
	SW3ICA185	291566	900	371	0	1	-,-	ASF-1 alternative splicing factor
	AS3ISB109	217787	nd	327	8	0	SL,A+	cytC reductase
	AS3ISA057	217676	nd	555	2	0	SL,-	NADH dehydrogenase (ubiquinone) chain CI-13
	SW3ICA294	309253	1000	409	0	3	-,-	NADH dehydrogenase (ubiquinone) chain 1
	SW3ICA404	343566	700	322	0	1	-,-	NADH dehydrogenase (ubiquinone) chain 2
f	Protein domains
	AS3ISA017	217653	nd	421	2	1	SL,-	fibronectin type III repeat
	AS3ISB040	217704	nd	379	2	1	SL,-	LIM domain protein
	AS3ISB350	281854	nd	92	1	0	SL,A+	MAD box homologue
	SW3ICA020	217588	200	226	0	1	-,-	GTP binding protein
	SW3ICA159	291558	1100	357	0	1	-,-	Retinoblastoma binding protein I domain
	SW3ICA170	291573	2500	401	0	1	-,-	Ca2+-transporting ATPase domain
	SW3ICA188	291568	800	372	0	1	-,-	calcium binding protein (calponin-like)
	SW3ICA232	291606	1500	200	0	1	-,-	immunoglobulin domain
	SW3ICA408	344489	1100	404	0	1	-,-	Ca2+-transporting ATPase domain
	SW3ICA421	354100	400	240	0	1	-,-	immunoglobulin domain
	SW3ICA229	291604	1000	355	0	2	-,-	Acanthocheilonema viteae protease inhibitor Av33
	SW3ICA092	217730	700	550	0	8	-,-	Ancylostoma caninum L3 secreted protein
	SW3ICA100	217602	700	567	0	2	-,-	Brugia malayi antigen SPX-1
	SW3ICA455	354133	800	476	0	1	-,-	Brugia malayi potentially protective 63 kd antigen
	SW3ICA396	343560	900	588	0	3	SL,-	Brugia malayi SL-transpliced L3 transcript BmYP44
	AS3ISB190	281215	400	412	2	1	SL,A+	Dirofilaria immitis cd31s filarial common antigen
	SW3ICA038	217600	600	328	0	4	-,-	Onchocerca volvulus cystatin variant 1
	AS3ISB061	217777	nd	522	5	0	SL,A+	Onchocerca volvulus cystatin variant 2
	AS3ISA056	217667	nd	200	1	0	SL,-	Onchocerca volvulus Ov16 PE binding protein
	SW3ICA257	291646	2500	317	0	1	-,-	Onchocerca volvulus embryonic antigen OVT1
	AS3ISA009	217660	nd	339	1	0	SL,-	mer-5 alkyl hydroperoxidase type 1
	AS3ISB135	217792	nd	330	1	2	SL,-	mer-5 alkyl hydroperoxidase type 2
	AS3ISB159	281194	nd	350	1	0	SL,-	cyclophilin/rotamase
	SW3ICA414	354094	700	507	0	1	-,-	murine heat shock protein 27
	AS3ISB220	281217	nd	575	1	0	SL,A+	macrophage migration inhibition factor
h	Homologues of C. elegans genes
	SW3ICA361	343520	350	353	0	1	-,-	BO416.5 gene product
	SW3ICA435	354113	450	309	0	1	-,-	C06A1.4 gene product
	SW3ICA375	343553	1400	450	0	1	-,-	C18H9.5 gene product
	SW3ICA232	291606	1500	200	0	1	-,-	C32D5.12 gene product
	AS3ISB062	217776	nd	346	1	0	SL,-	C32D5.7 gene product
	SW3ICA374	345329	300	469	0	1	-,-	C32D5.8 gene product
	SW3ICA322	320163	nd	307	0	1	-,-	C40H1.5 gene product
	SW3ICA030	217595	700	231	0	1	-,-	F53A9.10/C14F5.5 gene product (E rich)
	SW3ICA008	217580	1500	179	0	1	-,-	K01C8.9 gene product
	SW3ICA279	291636	2500	383	0	1	-,-	M28.6 gene product
	SW3ICA119	217614	800	365	0	1	-,-	T04A8.4 gene product
	SW3ICA418	354098	600	526	0	1	-,-	T04A8.6 gene product
	SW3ICA373	343552	300	320	0	1	-,-	T22H6.1 gene product
	AS3ISB021	217699	nd	512	4	0	SL,A+	T26A5.9 gene product
	AS3ISB132	217793	nd	316	1	0	SL,-	ZK1098.7 gene product
	SW3ICA104	217604	800	390	0	1	-,-	ZK353.1 gene product
	AS3ISB259	281265	nd	437	1	0	SL,-	ZK353.8 gene product
	AS3ISB022	217698	nd	366	3	0	SL,-	ZK652.2 gene product
	SW3ICA015	217585	800	396	0	3	SL,-	ZK673.8 gene product
	SW3ICA036	217599	600	293	0	1	-,-	C.elegans ESTs T01297
	AS3ISB023	217697	nd	445	8	0	SL,-	cuticle collagen precursor
	(5 clones)	-	-	-	1	4	-	various cuticle collagens
i	Clones unique to this dataset
	Abundant clones unique to this dataset
	AS3ISA010	217659		532	10	4	SL, A+
	SW3ICA096	217616	>2000	509	0	12	-,-
	AS3ISA027	217669		379	11	0	SL, A+	small possibly secreted protein, Tyr-rich
	AS3ISA033	217666		445	10	0	SL, A+	small possibly secreted protein
	AS3ISA030	217667		358	7	2	SL, A+	Glu-rich
	AS3ISB109	217787		327	8	0	SL, A+
	SW3ICA024	217726	600	387	0	8	-,-
	SW3ICA022	217590	600	296	0	5	-,-
	AS3ISA023	217672		485	4	0	SL, A+
	AS3ISB072	217770		427	4	0	SL, A+
	AS3ISA096	217690		265	3	0	SL, -	Tyr-rich
	AS3ISB337	281845		505	3	0	SL, -
	Other clones unique to this dataset
	226 clones representing 198 different sequences

NOTES to Table 2

(a) clone families are named by the first-sequenced member.
(b) dbest accession numbers of families of clones refer to the first-sequenced clone.
(c) length of insert determined by PCR (conventional library clones only; nd = not determined).
(d) length given for clone families is of longest read or of contig.
(e) other sequenced clones with >95% identity to the named clone from the SL1-dT cDNA library (SL1) or from the conventional cDNA library (conv.).
(f) while all clones are expected to have a poly(A) tail (as they were made using an oligo(dT) primer), its presence is noted only if it has been identified in the sequence. Some clones were found to terminate at internal restriction sites.
(g) a similarity was classesd as a "hit" when the BLAST score obtained had a probability of 1 x 10-5, except when (i) a high score was due to homopolymeric residue tracts (eg clone AS3ISA030), when the similarity was ignored, or (ii) the similarity was poor but was due to the conservation of residues defining a protein domain (eg AS3ISB040 and AS3ISB350), when the similarity to a domain is noted.