[Bioperl-l] problems running Bio::SearchIO on the FASTA results
Christie Robertson
cpr at geospiza.com
Mon Dec 27 18:53:35 EST 2004
Hi folks,
I'm wondering if anybody here is currently parsing the results of
the FASTA program with Bio::SearchIO. I'm running into a problem very
early on in the process, right at the moment of trying to parse a result.
Here is a pared-down example program:
>>>>>>
use Bio::SearchIO;
my $fastaFile = 'chWnt3_hg_Gnomon_prots_E0.001.out';
my $searchIO = new Bio::SearchIO(-format => 'fasta',
-file => $fastaFile);
my $result = $searchIO->next_result;
<<<<<<<
This program dies on the call to $searchIO->next_result() with this
message:
>>>>>>>
1039 cpr at napa:~/fastaTest > ./bioperlFastaParseTest.pl
Use of uninitialized value in concatenation (.) or string at
/usr/lib/perl5/site_perl/5.8.0/Bio/Search/HSP/GenericHSP.pm line 231,
<GEN1> line 131.
------------- EXCEPTION -------------
MSG: Did not specify a Query End or Query Begin -verbose 0 -algorithm
FASTP -hit_seq
CRNYIEIMPSVAEGVKLGIQECQHQFRGRRWNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNKHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDFLKDKYDSASEMVVEKHRESRGWVETLRAKYSLFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRIYDVHTCK
-hit_length 297 -query_length 297 -query_frame 0 -rank 1 -hit_name hmm6623
-query_name gi|18091804|gb|AAL58093.1| -evalue 0 -score 4361.0 -hit_frame
0 -hsp_length 297 -swscore 3215 -query_seq
WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
-homology_seq
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::
-bits 815.4 (qs='
STACK Bio::Search::HSP::GenericHSP::new
/usr/lib/perl5/site_perl/5.8.0/Bio/Search/HSP/GenericHSP.pm:231
STACK Bio::Search::HSP::FastaHSP::new
/usr/lib/perl5/site_perl/5.8.0/Bio/Search/HSP/FastaHSP.pm:97
STACK Bio::Factory::ObjectFactory::create_object
/usr/lib/perl5/site_perl/5.8.0/Bio/Factory/ObjectFactory.pm:150
STACK Bio::SearchIO::SearchResultEventBuilder::end_hsp
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/SearchResultEventBuilder.pm:275
STACK Bio::SearchIO::fasta::end_element
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/fasta.pm:872
STACK Bio::SearchIO::fasta::next_result
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/fasta.pm:403
STACK toplevel ./bioperlFastaParseTest.pl:9
--------------------------------------
1040 cpr at napa:~/fastaTest >
<<<<<<<
Apparently, Bio::Search::HSP::GenericHSP.pm expects Query End and Query
Begin to be set, and isn't getting them. Out of curiosity, I commented
the die line (231) from GenericHSP.pm, and then the module dies on the
next line, looking for Hit Begin and Hit End. Did the FASTA output format
get out of sync with SearchIO? Am I missing something?
I am attaching my output file.
Thanks for any help!
Christie
~~~~~~~~~~~~~~~~~~~~~~~~~
Christie P Robertson, PhD
Research Associate
Geospiza, Inc.
cpr at geospiza.com
(206)633-4403
~~~~~~~~~~~~~~~~~~~~~~~~~
-------------- next part --------------
# fasta chWnt3.fasta /usr/local/data/hg_Gnomon_prots.fsa 1 -E 0.001 -Q -s P20
FASTA searches a protein or DNA sequence data bank
version 3.4t24 July 21, 2004
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
Query library chWnt3.fasta vs /usr/local/data/hg_Gnomon_prots.fsa library
searching /usr/local/data/hg_Gnomon_prots.fsa library
1>>>gi|18091804|gb|AAL58093.1| Wnt3 [Gallus gallus] - 267 aa
vs /usr/local/data/hg_Gnomon_prots.fsa library
opt E()
< 20 1 0:=
22 2 0:= one = represents 62 library sequences
24 8 0:=
26 43 1:*
28 94 9:*=
30 295 52:*====
32 526 200:===*=====
34 791 543:========*====
36 844 1115:============== *
38 1300 1843:===================== *
40 2554 2571:=========================================*
42 3522 3142:==================================================*======
44 3683 3466:=======================================================*====
46 3282 3530:===================================================== *
48 3115 3380:=================================================== *
50 2902 3084:=============================================== *
52 2509 2711:========================================= *
54 2338 2316:=====================================*
56 2088 1935:===============================*==
58 1837 1588:=========================*====
60 1427 1287:====================*===
62 998 1031:================*
64 809 820:=============*
66 546 648:========= *
68 434 510:======= *
70 370 400:======*
72 303 312:=====*
74 266 243:===*=
76 183 190:===*
78 95 147:==*
80 83 114:=*
82 62 87:=*
84 71 69:=*
86 56 54:*
88 52 41:* inset = represents 1 library sequences
90 28 32:*
92 14 25:* :============== *
94 10 19:* :========== *
96 12 15:* :============ *
98 6 12:* :====== *
100 10 9:* :========*=
102 3 7:* :=== *
104 5 5:* :====*
106 5 4:* :===*=
108 1 3:* := *
110 0 2:* : *
112 0 2:* : *
114 0 1:* :*
116 0 1:* :*
118 0 1:* :*
>120 22 1:* :*=====================
17173199 residues in 37605 sequences
Expectation_n fit: rho(ln(x))= 1.9310+/-0.000241; mu= 29.4800+/- 0.014
mean_var=54.1966+/-10.424, 0's: 0 Z-trim: 22 B-trim: 0 in 0/45
Lambda= 0.174216
Kolmogorov-Smirnov statistic: 0.0254 (N=29) at 34
FASTA (3.47 Mar 2004) function [optimized, MD20 matrix (18:-29)] ktup: 1
join: 42, opt: 30, gap-pen: -26/-4, width: 32
Scan time: 6.780
The best scores are: opt bits E(37605)
hmm6623 Gene predicted by Gnomon on Homo sapiens ( 453) 3215 815.4 0
hmm10855 Gene predicted by Gnomon on Homo sapiens ( 352) 2746 697.3 4.4e-201
hmm9156 Gene predicted by Gnomon on Homo sapiens ( 351) 899 233.0 2.5e-61
hmm2415 Gene predicted by Gnomon on Homo sapiens ( 370) 814 211.7 6.8e-55
hmm19724 Gene predicted by Gnomon on Homo sapiens ( 360) 711 185.8 4.2e-47
hmm18663 Gene predicted by Gnomon on Homo sapiens ( 360) 711 185.8 4.2e-47
hmm12279 Gene predicted by Gnomon on Homo sapiens ( 865) 703 184.7 2.3e-46
hmm13855 Gene predicted by Gnomon on Homo sapiens ( 349) 652 171.0 1.2e-42
hmm9892 Gene predicted by Gnomon on Homo sapiens ( 391) 610 160.5 1.9e-39
hmm14214 Gene predicted by Gnomon on Homo sapiens ( 380) 606 159.5 3.7e-39
hmm2064 Gene predicted by Gnomon on Homo sapiens ( 411) 526 139.5 4.3e-33
hmm627 Gene predicted by Gnomon on Homo sapiens r ( 351) 518 137.3 1.7e-32
hmm2414 Gene predicted by Gnomon on Homo sapiens ( 389) 514 136.4 3.4e-32
hmm19734 Gene predicted by Gnomon on Homo sapiens ( 365) 469 125.0 8.6e-29
hmm18673 Gene predicted by Gnomon on Homo sapiens ( 365) 469 125.0 8.6e-29
hmm16428 Gene predicted by Gnomon on Homo sapiens ( 355) 446 119.2 4.7e-27
hmm13573 Gene predicted by Gnomon on Homo sapiens ( 587) 391 105.9 8e-23
hmm13572 Gene predicted by Gnomon on Homo sapiens ( 709) 378 102.8 8.2e-22
hmm1658 Gene predicted by Gnomon on Homo sapiens ( 354) 363 98.3 8.9e-21
hmm10853 Gene predicted by Gnomon on Homo sapiens ( 365) 170 49.9 3.6e-06
hmm6624 Gene predicted by Gnomon on Homo sapiens ( 357) 165 48.6 8.5e-06
>>hmm6623 Gene predicted by Gnomon on Homo sapiens refer (453 aa)
initn: 3215 init1: 3215 opt: 3215 Z-score: 4361.0 bits: 815.4 E(): 0
Smith-Waterman score: 3215; 98.502% identity (99.625% similar) in 267 aa overlap (1-267:187-453)
10 20 30
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAI
::::::::::::::::::::::::::::::
hmm662 CRNYIEIMPSVAEGVKLGIQECQHQFRGRRWNCTTIDDSLAIFGPVLDKATRESAFVHAI
160 170 180 190 200 210
40 50 60 70 80 90
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAREN
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
hmm662 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAREN
220 230 240 250 260 270
100 110 120 130 140 150
gi|180 RPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKY
:::::::::.::::::::::::::::::::::::::::::::::::::::::::.:::::
hmm662 RPDARSAMNKHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDFLKDKY
280 290 300 310 320 330
160 170 180 190 200 210
gi|180 DSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDR
::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::
hmm662 DSASEMVVEKHRESRGWVETLRAKYSLFKPPTERDLVYYENSPNFCEPNPETGSFGTRDR
340 350 360 370 380 390
220 230 240 250 260
gi|180 TCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
:::::::::::::::::::::::::::::::::::::::::::::::::.:::::::
hmm662 TCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRIYDVHTCK
400 410 420 430 440 450
>>hmm10855 Gene predicted by Gnomon on Homo sapiens refe (352 aa)
initn: 2746 init1: 2746 opt: 2746 Z-score: 3724.6 bits: 697.3 E(): 4.4e-201
Smith-Waterman score: 2746; 87.640% identity (90.262% similar) in 267 aa overlap (1-267:86-352)
10 20 30
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAI
:::::. :::::::::::::::::::::::
hmm108 CRNYVEIMPSVAEGIKIGIQECQHQFRGRRWNCTTVHDSLAIFGPVLDKATRESAFVHAI
60 70 80 90 100 110
40 50 60 70 80 90
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAREN
::::::::::::::::: :::: : : : :: :::::::::: .:: :::::::::::
hmm108 ASAGVAFAVTRSCAEGTAAICGCSSRHQGSPGKGWKWGGCSEDIEFGGMVSREFADAREN
120 130 140 150 160 170
100 110 120 130 140 150
gi|180 RPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKY
::::::::::::::::: : :::::::::::::::::::::: :::::::::.:::::
hmm108 RPDARSAMNRHNNEAGRQAIASHMHLKCKCHGLSGSCEVKTCWWSQPDFRAIGDFLKDKY
180 190 200 210 220 230
160 170 180 190 200 210
gi|180 DSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDR
:::::::::::::::::::::: .: :: :::::::::: :::::::::::::::::::
hmm108 DSASEMVVEKHRESRGWVETLRPRYTYFKVPTERDLVYYEASPNFCEPNPETGSFGTRDR
240 250 260 270 280 290
220 230 240 250 260
gi|180 TCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
:::: ::::::::::::::::: : :.:.::: :.:::::::::::: :::::::::
hmm108 TCNVSSHGIDGCDLLCCGRGHNARAERRREKCRCVFHWCCYVSCQECTRVYDVHTCK
300 310 320 330 340 350
>>hmm9156 Gene predicted by Gnomon on Homo sapiens refer (351 aa)
initn: 954 init1: 393 opt: 899 Z-score: 1215.7 bits: 233.0 E(): 2.5e-61
Smith-Waterman score: 899; 53.676% identity (58.456% similar) in 272 aa overlap (1-266:87-350)
10 20 30
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAI
::: : : :: .:: : ::: :::.::
hmm915 CKRNLEVMDSVRRGAQLAIEECQYQFRNRRWNCSTLD-SLPVFGKVVTQGTREAAFVYAI
60 70 80 90 100 110
40 50 60 70 80 90
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAREN
:::::::::: : : :::: : : : :::. .:: : : : ::
hmm915 SSAGVAFAVTRACSSGELEKCGCDRTVHGVSPQGFQWSGCSDNIAYGVAFSQSFVDVRER
120 130 140 150 160 170
100 110 120 130 140
gi|180 RPDARSA---MNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLK
: : :: ::::::: :: :: ::::: :::::::::: : : :: .: ::
hmm915 SKGASSSRALMNLHNNEAGRKAILTHMRVECKCHGVSGSCEVKTCWRAVPPFRQVGHALK
180 190 200 210 220 230
150 160 170 180 190 200
gi|180 DKYDSASEMVVEKHRESRGWVETLRA---KYALFKPPTERDLVYYENSPNFCEPNPETGS
.:.: : : :: : : :: . : ::: :. :::: : :: ::: :
hmm915 EKFDGATE--VEPRR-----VGSSRALVPRNAQFKPHTDEDLVYLEPSPDFCEQDMRSGV
240 250 260 270 280
210 220 230 240 250 260
gi|180 FGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVH
::: :::: :: ::::.::::::: : :.: : :::::.: : : : . :
hmm915 LGTRGRTCNKTSKAIDGCELLCCGRGFHTAQVELAERCSCKFHWCCFVKCRQCQRLVELH
290 300 310 320 330 340
gi|180 TCK
::
hmm915 TCR
350
>>hmm2415 Gene predicted by Gnomon on Homo sapiens refer (370 aa)
initn: 927 init1: 554 opt: 814 Z-score: 1100.1 bits: 211.7 E(): 6.8e-55
Smith-Waterman score: 814; 52.282% identity (58.091% similar) in 241 aa overlap (22-257:122-360)
10 20 30 40 50
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTIC
:: ::. :: :::: : ::: :: :
hmm241 ECKWQFRNRRWNCPTAPGPHLFGKIVNRGCRETAFIFAITSAGVTHSVARSCSEGSIESC
100 110 120 130 140 150
60 70 80 90 100 110
gi|180 GCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRTTIL
:: .:: : : :::::. ::: : ::: : : : : :: :::::::::.
hmm241 TCDYRRRGPGGPDWHWGGCSDNIDFGRLFGREFVDSGEKGRDLRFLMNLHNNEAGRTTVF
160 170 180 190 200 210
120 130 140 150 160
gi|180 DHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEK---HRESRGWV
: ::::: :::: :.::: : ::.:: :.:..: :: : ::
hmm241 SEMRQECKCHGMSGSCTVRTCWMRLPTLRAVGDVLRDRFDGASRVLYGNRGSNRASR--A
220 230 240 250 260
170 180 190 200 210 220
gi|180 ETLR--AKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLC
: :: ::: ::::.: ::::: : :: : :: : :::.:::
hmm241 ELLRLEPEDPAHKPPSPHDLVYFEKSPNFCTYSGRLGTAGTAGRACNSSSPALDGCELLC
270 280 290 300 310 320
230 240 250 260
gi|180 CGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
::::: ::: . :.: : :::::.::: :
hmm241 CGRGHRTRTQRVTERCNCTFHWCCHVSCRNCTHTRVLHECL
330 340 350 360 370
>>hmm19724 Gene predicted by Gnomon on Homo sapiens HSC_ (360 aa)
initn: 892 init1: 418 opt: 711 Z-score: 960.3 bits: 185.8 E(): 4.2e-47
Smith-Waterman score: 711; 48.718% identity (54.945% similar) in 273 aa overlap (1-267:85-349)
10 20 30
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAI
::: : : :: :: . ::::::.::
hmm197 CHRHPDVMRAISQGVAEWTAECQHQFRQHRWNCNTLDRDHSLFGRVLLRSSRESAFVYAI
60 70 80 90 100 110
40 50 60 70 80
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWK----WGGCSEDADFGVLVSREFAD
:::: ::.:: : : : :: : . : :::::. :.:. : : :
hmm197 SSAGVVFAITRACSQGEVKSCSCDPKKMGSAKDS-KGIFDWGGCSDNIDYGIKFARAFVD
120 130 140 150 160 170
90 100 110 120 130 140
gi|180 ARENRP-DARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDY
:.: . ::: :: ::: ::: . ::::: :::: .::: : ::: :::
hmm197 AKERKGKDARALMNLHNNRAGRKAVKRFLKQECKCHGVSGSCTLRTCWLAMADFRKTGDY
180 190 200 210 220 230
150 160 170 180 190 200
gi|180 LKDKYDSASEMVVEKHRESRGW-VETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGS
: :: : : . : : : :: :: ::::.:::: .: : ::
hmm197 LWRKYNGAIQVVM--NQDGTGFTVANER-----FKKPTKNDLVYFENSPDYCIRDREAGS
240 250 260 270 280
210 220 230 240 250 260
gi|180 FGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVH
:: : :: :: : : :. :::::. : : :: : ::::: : ::.: :::
hmm197 LGTAGRVCNLTSRGMDSCEVMCCGRGYDTSHVTRMTKCGCKFHWCCAVRCQDCLEALDVH
290 300 310 320 330 340
gi|180 TCK
:::
hmm197 TCKAPKNADWTTAT
350 360
>>hmm18663 Gene predicted by Gnomon on Homo sapiens refe (360 aa)
initn: 892 init1: 418 opt: 711 Z-score: 960.3 bits: 185.8 E(): 4.2e-47
Smith-Waterman score: 711; 48.718% identity (54.945% similar) in 273 aa overlap (1-267:85-349)
10 20 30
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAI
::: : : :: :: . ::::::.::
hmm186 CHRHPDVMRAISQGVAEWTAECQHQFRQHRWNCNTLDRDHSLFGRVLLRSSRESAFVYAI
60 70 80 90 100 110
40 50 60 70 80
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWK----WGGCSEDADFGVLVSREFAD
:::: ::.:: : : : :: : . : :::::. :.:. : : :
hmm186 SSAGVVFAITRACSQGEVKSCSCDPKKMGSAKDS-KGIFDWGGCSDNIDYGIKFARAFVD
120 130 140 150 160 170
90 100 110 120 130 140
gi|180 ARENRP-DARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDY
:.: . ::: :: ::: ::: . ::::: :::: .::: : ::: :::
hmm186 AKERKGKDARALMNLHNNRAGRKAVKRFLKQECKCHGVSGSCTLRTCWLAMADFRKTGDY
180 190 200 210 220 230
150 160 170 180 190 200
gi|180 LKDKYDSASEMVVEKHRESRGW-VETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGS
: :: : : . : : : :: :: ::::.:::: .: : ::
hmm186 LWRKYNGAIQVVM--NQDGTGFTVANER-----FKKPTKNDLVYFENSPDYCIRDREAGS
240 250 260 270 280
210 220 230 240 250 260
gi|180 FGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVH
:: : :: :: : : :. :::::. : : :: : ::::: : ::.: :::
hmm186 LGTAGRVCNLTSRGMDSCEVMCCGRGYDTSHVTRMTKCGCKFHWCCAVRCQDCLEALDVH
290 300 310 320 330 340
gi|180 TCK
:::
hmm186 TCKAPKNADWTTAT
350 360
>>hmm12279 Gene predicted by Gnomon on Homo sapiens refe (865 aa)
initn: 675 init1: 544 opt: 703 Z-score: 947.1 bits: 184.7 E(): 2.3e-46
Smith-Waterman score: 703; 53.361% identity (58.403% similar) in 238 aa overlap (22-254:618-852)
10 20 30 40 50
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTIC
:: :: .:: :::: ::: : : :
hmm122 ECQYQFRFGRWNCSALGEKTVFGQELRVGSREAAFTYAITAAGVAHAVTAACSQGNLSNC
590 600 610 620 630 640
60 70 80 90 100
gi|180 GCDSHHKG--PPGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRTT
::: : ::::::::: : .:. :: : :::: . :: :: :::::::
hmm122 GCDREKQGYYNQAEGWKWGGCSADVRYGIDFSRRFVDAREIKKNARRLMNLHNNEAGRKV
650 660 670 680 690 700
110 120 130 140 150 160
gi|180 ILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHRESRGWVE
: :.: ::::: :::: :::: : :: .: ::.:: : :: : ::
hmm122 LEDRMQLECKCHGVSGSCTTKTCWTTLPKFREVGHLLKEKYNAAVQ--VEVVRASRLRQP
710 720 730 740 750 760
170 180 190 200 210 220
gi|180 T-LRAKYAL--FKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLC
: :: : : . : : :::: : :::.:: ::: :: : :: :: : :::: :
hmm122 TFLRIK-QLRSYQKPMETDLVYIEKSPNYCEEDAATGSVGTQGRLCNRTSPGADGCDTMC
770 780 790 800 810 820
230 240 250 260
gi|180 CGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
::::.:: . : : :::::.: :
hmm122 CGRGYNTHQYTKVWQCNCKFHWCCFVKCNTCSERTEVFTCK
830 840 850 860
>>hmm13855 Gene predicted by Gnomon on Homo sapiens refe (349 aa)
initn: 592 init1: 483 opt: 652 Z-score: 880.2 bits: 171.0 E(): 1.2e-42
Smith-Waterman score: 652; 52.101% identity (57.563% similar) in 238 aa overlap (22-254:102-336)
10 20 30 40 50
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTIC
:: :: .:: :::: :.: : : :
hmm138 ECQFQFRNGRWNCSALGERTVFGKELKVGSREAAFTYAIIAAGVAHAITAACTQGNLSDC
80 90 100 110 120 130
60 70 80 90 100
gi|180 GCDSHHKGP--PGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRTT
::: : ::::::::: : .:. . : :::: . :: :: :::::::
hmm138 GCDKEKQGQYHRDEGWKWGGCSADIRYGIGFAKVFVDAREIKQNARTLMNLHNNEAGRKI
140 150 160 170 180 190
110 120 130 140 150 160
gi|180 ILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMV-VEKHRESRGWV
. : : ::::: :::: :::: : :: : ::::: : : :: : ::
hmm138 LEENMKLECKCHGVSGSCTTKTCWTTLPQFRELGYVLKDKYN---EAVHVEPVRASRNKR
200 210 220 230 240
170 180 190 200 210 220
gi|180 ET-LRAKYAL-FKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLC
: :. : : .. : . :::: : :::.:: : ::: :: : :: : :::: :
hmm138 PTFLKIKKPLSYRKPMDTDLVYIEKSPNYCEEDPVTGSVGTQGRACNKTAPQASGCDLMC
250 260 270 280 290 300
230 240 250 260
gi|180 CGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
::::.:: : : : ::::::: :
hmm138 CGRGYNTHQYARVWQCNCKFHWCCYVKCNTCSERTEMYTCK
310 320 330 340
>>hmm9892 Gene predicted by Gnomon on Homo sapiens refer (391 aa)
initn: 821 init1: 316 opt: 610 Z-score: 822.9 bits: 160.5 E(): 1.9e-39
Smith-Waterman score: 610; 45.588% identity (53.676% similar) in 272 aa overlap (1-267:116-380)
10 20 30
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAI
::::: : .:: : . :: :::.::
hmm989 CQRYPDIMRSVGEGAREWIRECQHQFRHHRWNCTTLDRDHTVFGRVMLRSSREAAFVYAI
90 100 110 120 130 140
40 50 60 70 80
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKG----PPGEGWKWGGCSEDADFGVLVSREFAD
:::: :.:: : : .: :: . .: :. :::::. .:: . : :
hmm989 SSAGVVHAITRACSQGELSVCSCDPYTRGRHHDQRGD-FDWGGCSDNIHYGVRFAKAFVD
150 160 170 180 190 200
90 100 110 120 130 140
gi|180 ARENRP-DARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDY
:.: : ::: :: ::: ::: . : ::::: :::: .::: : ::: :::
hmm989 AKEKRLKDARALMNLHNNRCGRTAVRRFLKLECKCHGVSGSCTLRTCWRALSDFRRTGDY
210 220 230 240 250 260
150 160 170 180 190 200
gi|180 LKDKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSF
:. .:: : : : . : ::::..::: .: ::
hmm989 LRRRYDGAVQVMATQDGAN---FTAARQGY---RRATRTDLVYFDNSPDYCVLDKAAGSL
270 280 290 300 310
210 220 230 240 250 260
gi|180 GTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHT
:: : : :: : :::. :::::. : : : : ::::: : : :: ::::
hmm989 GTAGRVCSKTSKGTDGCEIMCCGRGYDTTRVTRVTQCECKFHWCCAVRCKECRNTVDVHT
320 330 340 350 360 370
gi|180 CK
::
hmm989 CKAPKKAEWLDQT
380 390
>>hmm14214 Gene predicted by Gnomon on Homo sapiens refe (380 aa)
initn: 753 init1: 327 opt: 606 Z-score: 817.5 bits: 159.5 E(): 3.7e-39
Smith-Waterman score: 606; 47.761% identity (54.478% similar) in 268 aa overlap (1-257:113-370)
10 20 30
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAI
::: :.: .:: : :: :: .:.
hmm142 CHLYQDHMQYIGEGAKTGIKECQYQFRHRRWNCSTVDNT-SVFGRVMQIGSRETAFTYAV
90 100 110 120 130 140
40 50 60 70 80
gi|180 ASAGVAFAVTRSCAEGTSTICGC--DSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAR
::: : : : :: ::: : : . : :::: . :.: .:: :::
hmm142 SAAGVVNAMSRACREGELSTCGCSRAARPKDLPRD-WLWGGCGDNIDYGYRFAKEFVDAR
150 160 170 180 190 200
90 100 110 120 130 140
gi|180 E-NRPDAR----SA---MNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFR
: : :. :: :: ::::::: :. ::::: :::: :::: :::
hmm142 ERERIHAKGSYESARILMNLHNNEAGRRTVYNLADVACKCHGVSGSCSLKTCWLQLADFR
210 220 230 240 250 260
150 160 170 180 190 200
gi|180 AIGDYLKDKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNP
.:: ::.::::: : ::: : : :: :::: . :: .: :
hmm142 KVGDALKEKYDSAAAM----RLNSRG---KLVQVNSRFNSPTTQDLVYIDPSPDYCVRNE
270 280 290 300 310
210 220 230 240 250
gi|180 ETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNT-RTEKRKEKCHCIFHWCCYVSCQECIR
::: :: : :: :: : :::.: :::::. .: :.::: ::::::: : :
hmm142 STGSLGTQGRLCNKTSEGMDGCELMCCGRGYDQFKTVQ-TERCHCKFHWCCYVKCKKCTE
320 330 340 350 360 370
260
gi|180 VYDVHTCK
hmm142 IVDQFVCK
380
>>hmm2064 Gene predicted by Gnomon on Homo sapiens refer (411 aa)
initn: 691 init1: 299 opt: 526 Z-score: 708.7 bits: 139.5 E(): 4.3e-33
Smith-Waterman score: 526; 44.944% identity (53.558% similar) in 267 aa overlap (1-257:144-401)
10 20 30
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAI
::: : : .:: : :: :: ::.
hmm206 CQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCSTADNA-SVFGRVMQIGSRETAFTHAV
120 130 140 150 160 170
40 50 60 70 80
gi|180 ASAGVAFAVTRSCAEGTSTICGCD--SHHKGPPGEGWKWGGCSEDADFGVLVSREFADAR
::: :. : : :: ::: : : . : :::: . ..: .:: :::
hmm206 SAAGVVNAISRACREGELSTCGCSRTARPKDLPRD-WLWGGCGDNVEYGYRFAKEFVDAR
180 190 200 210 220 230
90 100 110 120 130 140
gi|180 E------NRPD--ARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFR
: . : :: .:::::: . ::::: :::: :::: .::
hmm206 EREKNFAKGSEEQGRVLMNLQNNEAGRRAVYKMADVACKCHGVSGSCSLKTCWLQLAEFR
240 250 260 270 280 290
150 160 170 180 190 200
gi|180 AIGDYLKDKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNP
.:: ::.::::: : : . .: : . : :: :::: . :: .: :
hmm206 KVGDRLKEKYDSAAAMRVTR----KGRLELVNSR---FTQPTPEDLVYVDPSPDYCLRNE
300 310 320 330 340
210 220 230 240 250 260
gi|180 ETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRV
::: :: : :: :: : :::.: :::::.: :.::: :::::.: : :
hmm206 STGSLGTQGRLCNKTSEGMDGCELMCCGRGYNQFKSVQVERCHCKFHWCCFVRCKKCTEI
350 360 370 380 390 400
gi|180 YDVHTCK
hmm206 VDQYICK
410
>>hmm627 Gene predicted by Gnomon on Homo sapiens refere (351 aa)
initn: 662 init1: 398 opt: 518 Z-score: 698.2 bits: 137.3 E(): 1.7e-32
Smith-Waterman score: 518; 53.333% identity (60.000% similar) in 135 aa overlap (20-153:81-215)
10 20 30 40
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTST
: :: :::::: :::: . :: : :
hmm627 IEECKYQFAWDRWNCPERALQLSSHGGLRSANRETAFVHAISSAGVMYTLTRNCSLGDFD
60 70 80 90 100 110
50 60 70 80 90 100
gi|180 ICGCDSHHKGPPG-EGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRT
:::: : : :: :::::. :: .:. : :: : ::: ::: :::::::
hmm627 NCGCDDSRNGQLGGQGWLWGGCSDNVGFGEAISKQFVDALETGQDARAAMNLHNNEAGRK
120 130 140 150 160 170
110 120 130 140 150 160
gi|180 TILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHRESRGWV
. : ::::: :::: ::: :.:: .: .::.:: :
hmm627 AVKGTMKRTCKCHGVSGSCTTQTCWLQLPEFREVGAHLKEKYHAALKVDLLQGAGNSAAG
180 190 200 210 220 230
170 180 190 200 210 220
gi|180 ETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLCCG
hmm627 RGAIADTFRSISTRELVHLEDSPDYCLENKTLGLLGTEGRECLRRGRALGRWERRSCRRL
240 250 260 270 280 290
>>hmm2414 Gene predicted by Gnomon on Homo sapiens refer (389 aa)
initn: 702 init1: 415 opt: 514 Z-score: 692.5 bits: 136.4 E(): 3.4e-32
Smith-Waterman score: 514; 49.485% identity (56.701% similar) in 194 aa overlap (65-257:194-379)
40 50 60 70 80 90
gi|180 VAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDA
: :::: : ::: ::.: : :: :
hmm241 LQALSRGKSFPHSLPSPGPGSSPSPGPQDTWEWGGCNHDMDFGEKFSRDFLDSREAPRDI
170 180 190 200 210 220
100 110 120 130 140 150
gi|180 RSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSAS
: ::: :: . . :::::: :::: :::: : :.:::.: :... :
hmm241 QARMRIHNNRVGRQVVTENLKRKCKCHGTSGSCQFKTCWRAAPEFRAVGAALRERLGRA-
230 240 250 260 270 280
160 170 180 190 200 210
gi|180 EMVVEKH-RESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCN
.. : : : :: . . : :::.: :: ::: : :: ::: : ::
hmm241 -IFIDTHNRNSGAFQPRLRPR----RLSGE--LVYFEKSPDFCERDPTMGSPGTRGRACN
290 300 310 320 330
220 230 240 250 260
gi|180 VTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
:: ::: :::::::: : :.::: ::::::: : ::
hmm241 KTSRLLDGCGSLCCGRGHNVLRQTRVERCHCRFHWCCYVLCDECKVTEWVNVCK
340 350 360 370 380
>>hmm19734 Gene predicted by Gnomon on Homo sapiens HSC_ (365 aa)
initn: 606 init1: 297 opt: 469 Z-score: 631.5 bits: 125.0 E(): 8.6e-29
Smith-Waterman score: 469; 45.136% identity (51.751% similar) in 257 aa overlap (21-267:117-365)
10 20 30 40 50
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTI
:.: ::..:. :: ::::: : :
hmm197 HERWNCMITAAATTAPMGASPLFGYELSSGTKETAFIYAVMAAGLVHSVTRSCSAGNMTE
90 100 110 120 130 140
60 70 80 90 100
gi|180 CGCDS--HHKGPPGEGWKWGGCSEDADFGVLVSREFAD-------ARENRPDARSAMNRH
: :: . : ::: :::::.: .: :: : : .::. ::: :
hmm197 CSCDTTLQNGGSASEGWHWGGCSDDVQYGMWFSRKFLDFPIGNTTGKENK--VLLAMNLH
150 160 170 180 190 200
110 120 130 140 150 160
gi|180 NNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKH
:::::: . : :.::: :::: ::::: : :: :::::.
hmm197 NNEAGRQAVAKLMSVDCRCHGVSGSCAVKTCWKTMSSFEKIGHLLKDKYENSIQISDKTK
210 220 230 240 250 260
170 180 190 200 210 220
gi|180 RESRGWVETLRAKYALFKPPTERD-LVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGID
: : : : : .: : : :::.: : :: : :: :: : :
hmm197 RKMRRREKDQR------KIPIHKDDLLYVNKSPNYCVEDKKLGIPGTQGRECNRTSEGAD
270 280 290 300 310
230 240 250 260
gi|180 GCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
:: :::::::.:: . :.: : : ::::: : : ::::::
hmm197 GCNLLCCGRGYNTHVVRHVERCECKFIWCCYVRCRRCESMTDVHTCK
320 330 340 350 360
>>hmm18673 Gene predicted by Gnomon on Homo sapiens refe (365 aa)
initn: 606 init1: 297 opt: 469 Z-score: 631.5 bits: 125.0 E(): 8.6e-29
Smith-Waterman score: 469; 45.136% identity (51.751% similar) in 257 aa overlap (21-267:117-365)
10 20 30 40 50
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTI
:.: ::..:. :: ::::: : :
hmm186 HERWNCMITAAATTAPMGASPLFGYELSSGTKETAFIYAVMAAGLVHSVTRSCSAGNMTE
90 100 110 120 130 140
60 70 80 90 100
gi|180 CGCDS--HHKGPPGEGWKWGGCSEDADFGVLVSREFAD-------ARENRPDARSAMNRH
: :: . : ::: :::::.: .: :: : : .::. ::: :
hmm186 CSCDTTLQNGGSASEGWHWGGCSDDVQYGMWFSRKFLDFPIGNTTGKENK--VLLAMNLH
150 160 170 180 190 200
110 120 130 140 150 160
gi|180 NNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKH
:::::: . : :.::: :::: ::::: : :: :::::.
hmm186 NNEAGRQAVAKLMSVDCRCHGVSGSCAVKTCWKTMSSFEKIGHLLKDKYENSIQISDKTK
210 220 230 240 250 260
170 180 190 200 210 220
gi|180 RESRGWVETLRAKYALFKPPTERD-LVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGID
: : : : : .: : : :::.: : :: : :: :: : :
hmm186 RKMRRREKDQR------KIPIHKDDLLYVNKSPNYCVEDKKLGIPGTQGRECNRTSEGAD
270 280 290 300 310
230 240 250 260
gi|180 GCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
:: :::::::.:: . :.: : : ::::: : : ::::::
hmm186 GCNLLCCGRGYNTHVVRHVERCECKFIWCCYVRCRRCESMTDVHTCK
320 330 340 350 360
>>hmm16428 Gene predicted by Gnomon on Homo sapiens refe (355 aa)
initn: 549 init1: 344 opt: 446 Z-score: 600.4 bits: 119.2 E(): 4.7e-27
Smith-Waterman score: 446; 51.128% identity (59.398% similar) in 133 aa overlap (20-151:81-213)
10 20 30 40
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTST
:::: :.::: :::: . .:. : :
hmm164 IEECKFQFAWERWNCPENALQLSTHNRLRSATRETSFIHAISSAGVMYIITKNCSMGDFE
60 70 80 90 100 110
50 60 70 80 90 100
gi|180 ICGCDSHHKGPPGE-GWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRT
:::: : : :: :::::. .:: .:. : : : ::: :: ::: :::
hmm164 NCGCDGSNNGKTGGHGWIWGGCSDNVEFGERISKLFVDSLEKGKDARALMNLHNNRAGRL
120 130 140 150 160 170
110 120 130 140 150 160
gi|180 TILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHRESRGWV
. : ::::: :::: . ::: .:: ::::: :::
hmm164 AVRATMKRTCKCHGISGSCSIQTCWLQLAEFREMGDYLKAKYDQALKIEMDKRQLRAGNS
180 190 200 210 220 230
170 180 190 200 210 220
gi|180 ETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLCCG
hmm164 AEGHWVPAEAFLPSAEAELIFLEESPDYCTCNSSLGIYGTEGRECLQNSHNTSRWERRSC
240 250 260 270 280 290
>>hmm13573 Gene predicted by Gnomon on Homo sapiens refe (587 aa)
initn: 726 init1: 344 opt: 391 Z-score: 524.4 bits: 105.9 E(): 8e-23
Smith-Waterman score: 391; 43.541% identity (49.761% similar) in 209 aa overlap (65-257:379-577)
40 50 60 70 80 90
gi|180 VAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDA
: ::::: : :: :..: : :: :
hmm135 LDALQRGKGLSHGVPEHPALPTASPGLQDSWEWGGCSPDMGFGERFSKDFLDSREPHRDI
350 360 370 380 390 400
100 110 120 130 140 150
gi|180 RSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSAS
: ::: :: . . : :::::: :::: :::: :.:: .: :. .. :
hmm135 HARMRLHNNRVGRQAVMENMRRKCKCHGTSGSCQLKTCWQVTPEFRTVGALLRSRFHRAT
410 420 430 440 450 460
160 170 180 190
gi|180 EMVVEKHRESRGWVET----------------LRAKYALFKPPTERDLVYYENSPNFCEP
. : : : :: : ::::.: :: :::
hmm135 --LIRPHNRNGGQLEPGPAGAPSPAPGAPGPRRRA------SPA--DLVYFEKSPDFCER
470 480 490 500 510
200 210 220 230 240 250
gi|180 NPETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECI
: : :: : :: : : ::: ::::::: : :.::: :::::.: : ::
hmm135 EPRLDSAGTVGRLCNKSSAGSDGCGSMCCGRGHNILRQTRSERCHCRFHWCCFVVCEECR
520 530 540 550 560 570
260
gi|180 RVYDVHTCK
hmm135 ITEWVSVCK
580
>>hmm13572 Gene predicted by Gnomon on Homo sapiens refe (709 aa)
initn: 641 init1: 295 opt: 378 Z-score: 506.2 bits: 102.8 E(): 8.2e-22
Smith-Waterman score: 378; 46.667% identity (51.795% similar) in 195 aa overlap (65-257:511-699)
40 50 60 70 80 90
gi|180 VAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRP--
: :::: .: ::: :: : ::: :
hmm135 PRGRAPPRPSGLPGTPGPPGPAGSPEGSAAWEWGGCGDDVDFGDEKSRLFMDARHKRGRG
490 500 510 520 530 540
100 110 120 130 140 150
gi|180 DARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDS
: : ::::::: . : :::::::::: .::: : :: .: : ...
hmm135 DIRALVQLHNNEAGRLAVRSHTRTECKCHGLSGSCALRTCWQKLPPFREVGARLLERFHG
550 560 570 580 590 600
160 170 180 190 200 210
gi|180 ASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTC
:: : . . : ::: :: : :: :: :: ::: ::: : :
hmm135 ASR-VMGTN-DGKALLPAVRT----LKPPGRADLLYAADSPDFCAPNRRTGSPGTRGRAC
610 620 630 640 650
220 230 240 250 260
gi|180 NVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
: ::::::::::: : : : ::::: : :. :
hmm135 NSSAPDLSGCDLLCCGRGHRQESVQLEENCLCRFHWCCVVQCHRCRVRKELSLCL
660 670 680 690 700
>>hmm1658 Gene predicted by Gnomon on Homo sapiens refer (354 aa)
initn: 497 init1: 351 opt: 363 Z-score: 487.6 bits: 98.3 E(): 8.9e-21
Smith-Waterman score: 363; 42.041% identity (51.020% similar) in 245 aa overlap (17-257:104-344)
10 20 30 40
gi|180 WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEG
:.. :::::::.: : . :. : : :
hmm165 REVMKACRRAFADMRWNCSSIELAPNYLLDLERGTRESAFVYALSAAAISHAIARACTSG
80 90 100 110 120 130
50 60 70 80 90 100
gi|180 TSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADA----RENRPDARSAMNRHN
: : ::: : .:::: . .: : : :: . : : ::
hmm165 DLPGCSCGPVPGEPPGPGNRWGGCADNLSYGLLMGAKFSDAPMKVKKTGSQANKLMRLHN
140 150 160 170 180 190
110 120 130 140 150 160
gi|180 NEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHR
: :: :::::: :::: ..::: . . :: .: :: : ::
hmm165 SEVGRQALRASLEMKCKCHGVSGSCSIRTCWKGLQELQDVAADLKTRYLSATKVV---HR
200 210 220 230 240 250
170 180 190 200 210 220
gi|180 ESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGC
: : : .: . .::: :: :: : :: :: :: :: :: : : :
hmm165 -PMGTRKHLVPKDLDIRPVKDSELVYLQSSPDFCMKNEKVGSHGTQDRQCNKTSNGSDSC
260 270 280 290 300
230 240 250 260
gi|180 DLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
:: :::::.: :.. :.::: .:::::: : :
hmm165 DLMCCGRGYNPYTDRVVERCHCKYHWCCYVTCRRCERTVERYVCK
310 320 330 340 350
>>hmm10853 Gene predicted by Gnomon on Homo sapiens refe (365 aa)
initn: 283 init1: 170 opt: 170 Z-score: 225.4 bits: 49.9 E(): 3.6e-06
Smith-Waterman score: 170; 55.556% identity (66.667% similar) in 36 aa overlap (118-153:215-250)
90 100 110 120 130 140
gi|180 RENRPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLK
::::: :::: :.::: : .: .::
hmm108 RRSSKDLRARVDFHNNLVGVKVIKAGVETTCKCHGVSGSCTVRTCWRQLAPFHEVGKHLK
190 200 210 220 230 240
150 160 170 180 190 200
gi|180 DKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGT
::. :
hmm108 HKYETALKVGSTTNEAAGEAGAISPPRGRASGAGGSDPLPRTPELVHLDDSPSFCLAGRF
250 260 270 280 290 300
>>hmm6624 Gene predicted by Gnomon on Homo sapiens refer (357 aa)
initn: 339 init1: 165 opt: 165 Z-score: 218.7 bits: 48.6 E(): 8.5e-06
Smith-Waterman score: 165; 81.250% identity (87.500% similar) in 16 aa overlap (118-133:210-225)
90 100 110 120 130 140
gi|180 RENRPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLK
::::: :::: :.:::
hmm662 KRGNKDLRARADAHNTHVGIKAVKSGLRTTCKCHGVSGSCAVRTCWKQLSPFRETGQVLK
180 190 200 210 220 230
150 160 170 180 190 200
gi|180 DKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGT
hmm662 LRYDSAVKVSSATNEALGRLELWAPARQGSLTKGLAPRSGDLVYMEDSPSFCRPSKYSPG
240 250 260 270 280 290
267 residues in 1 query sequences
17173199 residues in 37605 library sequences
Scomplib [34t24]
start: Mon Dec 27 15:38:25 2004 done: Mon Dec 27 15:38:32 2004
Total Scan time: 6.780 Total Display time: 0.030
Function used was FASTA [version 3.4t24 July 21, 2004]
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