geneid samples: homology information
1. Prediction ab initio
## gff-version 2
## date Mon Oct  8 09:48:32 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Optimal Gene Structure. 6 genes. Score = 161.724069 
# Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 
test	geneid_v1.2	Internal	3698	3982	 8.69	+	2	gene_1
test	geneid_v1.2	Internal	4612	4890	 5.95	+	2	gene_1
test	geneid_v1.2	Internal	5102	5230	 1.03	+	2	gene_1
test	geneid_v1.2	Internal	13675	13737	 0.26	+	2	gene_1
test	geneid_v1.2	Internal	15525	15806	 4.26	+	2	gene_1
test	geneid_v1.2	Internal	17034	17318	 3.80	+	2	gene_1
test	geneid_v1.2	Internal	21599	21618	 0.64	+	2	gene_1
test	geneid_v1.2	Terminal	23145	23375	 0.61	+	0	gene_1
# Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193 
test	geneid_v1.2	   First	74617	74854	 6.35	+	0	gene_2
test	geneid_v1.2	Terminal	74929	75233	 3.91	+	2	gene_2
# Gene 3 (Reverse). 5 exons. 197 aa. Score = 7.990742 
test	geneid_v1.2	Terminal	94916	95043	-0.44	-	2	gene_3
test	geneid_v1.2	Internal	95943	96084	 1.53	-	0	gene_3
test	geneid_v1.2	Internal	96314	96443	 2.43	-	1	gene_3
test	geneid_v1.2	Internal	97054	97185	 4.67	-	1	gene_3
test	geneid_v1.2	   First	98244	98302	-0.20	-	0	gene_3
# Gene 4 (Forward). 15 exons. 766 aa. Score = 46.549015 
test	geneid_v1.2	   First	101952	102061	-1.42	+	0	gene_4
test	geneid_v1.2	Internal	102210	102340	-0.15	+	1	gene_4
test	geneid_v1.2	Internal	103300	103505	 3.34	+	2	gene_4
test	geneid_v1.2	Internal	103932	104129	 4.76	+	0	gene_4
test	geneid_v1.2	Internal	105331	105459	 4.56	+	0	gene_4
test	geneid_v1.2	Internal	105609	105797	 3.81	+	0	gene_4
test	geneid_v1.2	Internal	106357	106530	 5.45	+	0	gene_4
test	geneid_v1.2	Internal	106774	106936	 1.28	+	0	gene_4
test	geneid_v1.2	Internal	107245	107381	 2.61	+	2	gene_4
test	geneid_v1.2	Internal	108664	108840	 2.52	+	0	gene_4
test	geneid_v1.2	Internal	111360	111507	 1.14	+	0	gene_4
test	geneid_v1.2	Internal	111666	111777	 4.83	+	2	gene_4
test	geneid_v1.2	Internal	112186	112315	 4.80	+	1	gene_4
test	geneid_v1.2	Internal	112714	112918	 6.00	+	0	gene_4
test	geneid_v1.2	Terminal	113402	113490	 3.02	+	2	gene_4
# Gene 5 (Forward). 15 exons. 1040 aa. Score = 51.141949 
test	geneid_v1.2	   First	116217	116709	 1.18	+	0	gene_5
test	geneid_v1.2	Internal	116799	116913	 4.26	+	2	gene_5
test	geneid_v1.2	Internal	117437	117484	 0.05	+	1	gene_5
test	geneid_v1.2	Internal	118677	118807	 3.22	+	1	gene_5
test	geneid_v1.2	Internal	119091	119296	 7.73	+	2	gene_5
test	geneid_v1.2	Internal	121626	121823	 6.17	+	0	gene_5
test	geneid_v1.2	Internal	121989	122117	 2.09	+	0	gene_5
test	geneid_v1.2	Internal	123644	123832	 2.08	+	0	gene_5
test	geneid_v1.2	Internal	124010	124183	 7.03	+	0	gene_5
test	geneid_v1.2	Internal	124361	124520	 3.46	+	0	gene_5
test	geneid_v1.2	Internal	132128	132308	 2.65	+	2	gene_5
test	geneid_v1.2	Internal	137494	137585	 1.72	+	1	gene_5
test	geneid_v1.2	Internal	139123	139392	 4.46	+	2	gene_5
test	geneid_v1.2	Internal	139835	140116	 3.25	+	2	gene_5
test	geneid_v1.2	Terminal	150538	150989	 1.80	+	2	gene_5
# Gene 6 (Forward). 6 exons. 314 aa. Score = 20.532181 
test	geneid_v1.2	   First	159435	159556	 0.89	+	0	gene_6
test	geneid_v1.2	Internal	177915	177947	 0.49	+	1	gene_6
test	geneid_v1.2	Internal	190046	190173	-1.22	+	1	gene_6
test	geneid_v1.2	Internal	192477	192743	17.00	+	2	gene_6
test	geneid_v1.2	Internal	195269	195550	 1.81	+	2	gene_6
test	geneid_v1.2	Internal	196514	196624	 1.56	+	2	gene_6
% geneid -G test.fasta


2. Introducing sequence homology information
## Homology information: HSP
test	BLASTN	HSP	74000	75500	 50.000	-	.
test	BLASTN	HSP	76000	76500	100.000	-	.
test	BLASTN	HSP	78000	79500	 50.000	-	.


## date Mon Oct  8 10:21:06 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Optimal Gene Structure. 6 genes. Score = 209.270570 
# Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 
Internal     3698     3982	 8.69	+ 2 1	 5.39	 1.69	23.61	 0.00	AA   1: 96 gene_1
Internal     4612     4890	 5.95	+ 2 1	 3.01	 2.36	19.33	 0.00	AA  96:189 gene_1
Internal     5102     5230	 1.03	+ 2 1	 0.20	 2.06	11.69	 0.00	AA 189:232 gene_1
Internal    13675    13737	 0.26	+ 2 1	 2.23	 5.66	 1.33	 0.00	AA 232:253 gene_1
Internal    15525    15806	 4.26	+ 2 1	 5.61	 2.81	11.79	 0.00	AA 253:347 gene_1
Internal    17034    17318	 3.80	+ 2 1	 5.76	 1.67	12.10	 0.00	AA 347:442 gene_1
Internal    21599    21618	 0.64	+ 2 0	 4.61	 5.66	-0.07	 0.00	AA 442:448 gene_1
Terminal    23145    23375	 0.61	+ 0 0	 5.33	 0.00	 7.28	 0.00	AA 449:525 gene_1

>test|geneid_v1.2_predicted_protein_1|525_AA
ctPTPMWPDDLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADW
AQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCF
VSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEI
DRYTAIAYWVPRNALPSDLLENVLCGVAFGLGVLGIIVGIVLIIYFRKPCSGEQSMITFL
PLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCE
FGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPF
NTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPS
YGDTYTCVVEHIGAPEPILRDWRKAVPFQADAGSKKKPGSMGAIQCHAGQHLRQTPGAEV
LRVGPEGQMEDRKYIHNKKEKRQCCGVEREVQNLGFFWPWTMTSA*


# Gene 2 (Reverse). 11 exons. 537 aa. Score = 51.309784 
Terminal    26805    26994	 0.68	- 1 0	 0.00	 0.27	15.05	 0.00	AA 474:537 gene_2
Internal    47107    47188	-0.31	- 2 2	 4.09	 1.96	 3.90	 0.00	AA 447:474 gene_2
Internal    70660    70831	 0.57	- 0 1	 2.22	 0.79	10.66	 0.00	AA 390:447 gene_2
Internal    73992    74191	 1.63	- 2 0	 2.48	-3.18	 2.88	 6.40	AA 323:389 gene_2
Internal    74475    74801	11.88	- 2 1	-1.55	 0.73	17.45	10.89	AA 214:323 gene_2
Internal    74925    75006	-0.62	- 0 1	-5.56	 6.63	 3.77	 2.73	AA 187:214 gene_2
Internal    76083    76212	18.65	- 1 0	-0.38	-6.11	 5.24	25.95	AA 143:186 gene_2
Internal    76337    76368	-0.07	- 0 2	-0.89	-0.67	-0.06	 6.39	AA 133:143 gene_2
Internal    76398    76516	18.53	- 2 0	-0.67	 2.24	 6.31	20.56	AA  93:132 gene_2
Internal    77306    77382	-2.88	- 1 1	 4.14	-2.09	 3.47	 0.00	AA  67: 93 gene_2
   First    78038    78237	 3.25	- 0 2	 2.39	-3.03	 6.19	 6.66	AA   1: 67 gene_2


>test|geneid_v1.2_predicted_protein_2|537_AA
MQDLQAKNYVMLVNDIKEDLFSLYLCGEKYCSWIGRFNIVNMSILPKPIYKFNTIPIKIF
ARFVNYRRVCGYFLRTQKRENQNQRVHEYMCTVLLLLNHFLHVLEELIGIDGQNKNFNIA
ANDRRVSERVPNVKDCMHVCGKEADIGASLTCEKKASFDEKKFSLFLVNTKKCNRNFKGS
RPENVTVRGHYPPLHCFLVPEPDTLAPSLQQQLIFVCWTICRQDVHFIPLLGFFAQLLVD
TPTGMFGRRHHRGSRRGVVLQDPLEGPLRGRGGRHCRVLRLSAQGRCLAWGPRTEGSALA
ETSRQTRSPLKAKAAAPAASEREVQKEVSGRKIAFFTNSELNNGEMEQLGIHRQDNKIKM
KLDLSLTPYAKFNSNWIGLLESRSSRPAWECKNKTVVKVLTKLYEGLGKIEKEKTIENSS
ILITDITDVRDHRLQSSKGSPTRNRPGKTLGFKNDFLEDNEITEIITGITEDS*HRKNIN
GAGTIEHSRAIGGEKDNKEEEKEEQQFNLRLIPSAKIDSIWITNFYAKCKTIKLLE*

# Gene 3 (Reverse). 7 exons. 298 aa. Score = 14.490652 
Terminal    78787    79006	 6.99	- 1 0	 0.00	 3.23	 8.30	 7.23	AA 225:298 gene_3
Internal    79267    79446	 0.97	- 1 2	-3.15	-3.00	10.41	 6.00	AA 165:225 gene_3
Internal    87121    87151	-1.90	- 2 2	-0.33	 5.16	 1.76	 0.00	AA 155:165 gene_3
Internal    95943    96084	 1.53	- 0 1	 1.04	 1.08	13.14	 0.00	AA 108:155 gene_3
Internal    96314    96443	 2.43	- 1 0	 5.34	 4.11	 4.41	 0.00	AA  64:107 gene_3
Internal    97054    97185	 4.67	- 1 2	 0.34	 2.74	19.56	 0.00	AA  20: 64 gene_3
   First    98244    98302	-0.20	- 0 2	 3.60	 1.52	 5.57	 0.00	AA   1: 20 gene_3

>test|geneid_v1.2_predicted_protein_3|298_AA
MAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAAYQL
ELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQVYGTLGGMLTRQP
FAIGGSGSTFIYGYVDAAYKPGMSPEECRRFTTDVKFLKQKWFRRKYLGTNSFNEEFYQR
FKEELTPINLFQKIEAEEAFPSLFYKARITSIPKPNNDNGKKRKLNIGVEEIFLYLIKIV
YKNPMVNILDSERLNSFYLKSGTRQECPLSPLLFTVLEVLDSAIGMKKEIKGIQIVK*

# Gene 4 (Forward). 15 exons. 766 aa. Score = 46.549015 
   First   101952   102061	-1.42	+ 0 2	 1.16	 0.34	 6.71	 0.00	AA   1: 37 gene_4
Internal   102210   102340	-0.15	+ 1 1	 4.04	-1.92	 8.94	 0.00	AA  37: 81 gene_4
Internal   103300   103505	 3.34	+ 2 0	 4.52	 4.14	 7.86	 0.00	AA  81:149 gene_4
Internal   103932   104129	 4.76	+ 0 0	 3.85	-0.04	18.67	 0.00	AA 150:215 gene_4
Internal   105331   105459	 4.56	+ 0 0	 5.35	 3.92	10.00	 0.00	AA 216:258 gene_4
Internal   105609   105797	 3.81	+ 0 0	 5.64	 0.78	12.40	 0.00	AA 259:321 gene_4
Internal   106357   106530	 5.45	+ 0 0	 3.90	 3.52	15.00	 0.00	AA 322:379 gene_4
Internal   106774   106936	 1.28	+ 0 1	 3.56	 0.52	 9.56	 0.00	AA 380:434 gene_4
Internal   107245   107381	 2.61	+ 2 0	 3.85	 4.71	 6.19	 0.00	AA 434:479 gene_4
Internal   108664   108840	 2.52	+ 0 0	 4.41	-1.36	14.21	 0.00	AA 480:538 gene_4
Internal   111360   111507	 1.14	+ 0 1	 4.01	 0.44	 8.68	 0.00	AA 539:588 gene_4
Internal   111666   111777	 4.83	+ 2 2	 4.40	 5.44	 9.82	 0.00	AA 588:625 gene_4
Internal   112186   112315	 4.80	+ 1 0	 3.55	 3.50	13.92	 0.00	AA 625:668 gene_4
Internal   112714   112918	 6.00	+ 0 1	 2.72	 1.65	20.97	 0.00	AA 669:737 gene_4
Terminal   113402   113490	 3.02	+ 2 0	 5.19	 0.00	12.26	 0.00	AA 737:766 gene_4

>test|geneid_v1.2_predicted_protein_4|766_AA
MAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQ
GEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIML
WGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFA
NEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSS
GNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEG
LVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ
LLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGA
HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV
EQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPT
EFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINP
YLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGS
MICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRA
IAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ*

# Gene 5 (Forward). 15 exons. 1040 aa. Score = 51.141949 
   First   116217   116709	 1.18	+ 0 1	 4.46	 2.44	 5.09	 0.00	AA   1:165 gene_5
Internal   116799   116913	 4.26	+ 2 2	 5.85	 4.63	 7.42	 0.00	AA 165:203 gene_5
Internal   117437   117484	 0.05	+ 1 2	 6.31	 3.70	-1.13	 0.00	AA 203:219 gene_5
Internal   118677   118807	 3.22	+ 1 1	 5.18	 3.05	 8.20	 0.00	AA 219:263 gene_5
Internal   119091   119296	 7.73	+ 2 0	 5.08	 4.49	17.47	 0.00	AA 263:331 gene_5
Internal   121626   121823	 6.17	+ 0 0	 4.30	 3.64	17.26	 0.00	AA 332:397 gene_5
Internal   121989   122117	 2.09	+ 0 0	 7.47	 4.49	 1.03	 0.00	AA 398:440 gene_5
Internal   123644   123832	 2.08	+ 0 0	 4.08	 0.30	11.14	 0.00	AA 441:503 gene_5
Internal   124010   124183	 7.03	+ 0 0	 5.53	 3.68	16.25	 0.00	AA 504:561 gene_5
Internal   124361   124520	 3.46	+ 0 1	 4.54	 1.41	12.22	 0.00	AA 562:615 gene_5
Internal   132128   132308	 2.65	+ 2 2	 6.44	 3.78	 5.05	 0.00	AA 615:675 gene_5
Internal   137494   137585	 1.72	+ 1 1	 5.36	 5.38	 1.95	 0.00	AA 675:706 gene_5
Internal   139123   139392	 4.46	+ 2 1	 2.30	 4.31	14.99	 0.00	AA 706:796 gene_5
Internal   139835   140116	 3.25	+ 2 1	 5.08	-0.18	13.27	 0.00	AA 796:890 gene_5
Terminal   150538   150989	 1.80	+ 2 0	 1.12	 0.00	16.56	 0.00	AA 890:1040 gene_5

>test|geneid_v1.2_predicted_protein_5|1040_AA
MRLPDLRPWTSLLLVDAALLWLLQGPLGTLLPQGLPGLWLEGTLRLGGLWGLLKLRGLLG
FVGTLLLPLCLATPLTVSLRALVAGASRAPPARVASAPWSWLLVGYGAAGLSWSLWAVLS
PPGAQEKEQDQVNNKVLMWRLLKLSRPDLPLLVAAFFFLVLAVLGETLIPHYSGRVIDIL
GGDFDPHAFASAIFFMCLFSFGRHTQTNKLFDKAGTGMSSLSAGCRGGCFTYTMSRINLR
IREQLFSSLLRQDLGFFQETKTGELNSRLSSDTTLMSNWLPLNANVLLRSLVKVVGLYGF
MLSISPRLTLLSLLHMPFTIAAEKVYNTRHQEVLREIQDAVARAGQVVREAVGGLQTVRS
FGAEEHEVCRYKEALEQCRQLYWRRDLERALYLLVRRVLHLGVQMLMLSCGLQQMQDGEL
TQGSLLSFMIYQESVGSYVQTLVYIYGDMLSNVGAAEKVFSYMDRQPNLPSPGTLAPTTL
QGVVKFQDVSFAYPNRPDRPVLKGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTG
GQVLLDEKPISQYEHCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAH
ADDFIQEMEHGIYTENPLEVHDILNFSGYFLGIMSSNERICGTKHHQHLFFQDEVMDKTI
TGKLRQIVHVKQYFGMGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTN
GTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVC
RHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEER
AGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWNAEKSSDKIQH
SFMLKTLDKLVIEGTYVKIVRAIYDKPAANIILNGQNLEAFPLKTGRRQECPLSLLLFNI
VLEVLARAIRQEKRIKSSQIGKEEVKVFLFADDMIIYLENPIVSAQKLLKLINNFSKVSG
YKINVQKLLIFLYTNNSQA*

# Gene 6 (Forward). 6 exons. 314 aa. Score = 20.532181 
   First   159435   159556	 0.89	+ 0 2	 1.25	 6.11	 4.94	 0.00	AA   1: 41 gene_6
Internal   177915   177947	 0.49	+ 1 2	 5.67	 4.44	-0.19	 0.00	AA  41: 52 gene_6
Internal   190046   190173	-1.22	+ 1 1	 2.30	 0.25	 6.88	 0.00	AA  52: 95 gene_6
Internal   192477   192743	17.00	+ 2 1	 4.16	 4.31	42.30	 0.00	AA  95:184 gene_6
Internal   195269   195550	 1.81	+ 2 1	 3.07	 1.41	11.56	 0.00	AA 184:278 gene_6
Internal   196514   196624	 1.56	+ 2 1	 2.68	 4.53	 5.59	 0.00	AA 278:314 gene_6

>test|geneid_v1.2_predicted_protein_6|314_AA
MRDKSSAWPHHQQSCYYNEDEGTEKRGRDGIHQTTVLIHTRDSMTFIHLVPRCTCFMVQG
GFKQLKNLQEKSQQILSLEEHECNTFLHNKESLAKDFLVQFKGMCYFTNGTERVRGVARY
IYNREEYGRFDSDVGEFQAVTELGRSIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTL
QRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNG
DWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLI
FLGLGLIIRHRGQKag

% geneid -GS sr.gff test.fasta





Enrique Blanco Garcia © 2003