[Bioperl-l] Problem with T-Coffee

Mon Aug 30 23:27:52 EDT 2004

Did you also symlink mocca and lalign2list in addition to t_coffee as 
those are also depended on by t_coffee?

-jason

On Aug 28, 2004, at 1:05 AM, Jonathan Manning wrote:

> Hi Jason,
>
> Thanks for the reply.
>
> My versions of Bioperl, Bioperl-run and T-Coffee are
> the same on both machines.
>
> When I run the test I get the following output:
>
>
> 1..22
> # Running under perl version 5.008 for linux
> # Current time local: Fri Aug 27 10:10:30 2004
> # Current time GMT:   Fri Aug 27 14:10:30 2004
> # Using Test.pm version 1.23
> ok 1
> ok 2
> ok 3
> ok 4
> ok 5
>
> Abnormal Program Termination:[T-COFFEE, Version_1.37]
> Please report the fault to:
> cedric.notredame at europe.com (Indicate the version nu
> mber)
> Thank you for your cooperation :-)
>
> ------------- EXCEPTION  -------------
> MSG: TCoffee call crashed: 256 [command
> /usr/bin/t_coffee -in=t/data/cysprot.fa,
> Xblosum,Mlalign_id_pair,Mclustalw_pair  -ktuple=3
> -output=clustalw -outfile=/tmp
> /MvE0LpuQko/mPn9bfUyI0 -quiet]
>
> STACK Bio::Tools::Run::Alignment::TCoffee::_run
> Bio/Tools/Run/Alignment/TCoffee.
> pm:814
> STACK Bio::Tools::Run::Alignment::TCoffee::align
> Bio/Tools/Run/Alignment/TCoffee
> .pm:719
> STACK toplevel t/TCoffee.t:62
>
> --------------------------------------
> ok 6 # skip TCoffee program not found. Skipping.
>
> ok 7 # skip TCoffee program not found. Skipping.
>
> ok 8 # skip TCoffee program not found. Skipping.
>
> ok 9 # skip TCoffee program not found. Skipping.
>
> ok 10 # skip TCoffee program not found. Skipping.
>
> ok 11 # skip TCoffee program not found. Skipping.
>
> ok 12 # skip TCoffee program not found. Skipping.
>
> ok 13 # skip TCoffee program not found. Skipping.
>
> ok 14 # skip TCoffee program not found. Skipping.
>
> ok 15 # skip TCoffee program not found. Skipping.
>
> ok 16 # skip TCoffee program not found. Skipping.
>
> ok 17 # skip TCoffee program not found. Skipping.
>
> ok 18 # skip TCoffee program not found. Skipping.
>
> ok 19 # skip TCoffee program not found. Skipping.
>
> ok 20 # skip TCoffee program not found. Skipping.
>
> ok 21 # skip TCoffee program not found. Skipping.
>
> ok 22 # skip TCoffee program not found. Skipping.
>
>
> I guess that explains something- it's not seeing the
> T-Coffee program for some reason. I don't know why it
> shouldn't- I placed it in /usr/bin using a soft-link
> (ln -s).
>
> Nothing unusual with my sequence file, but I'm
> attaching it anyway, and relevant snippet of code is
> below (it's a subroutine passed an arrayref of
> sequences):
>
>  sub align {
>
> 	# T-COFFEE USED TO CREATE A Bio::SimpleAlign OBJECT
>
>     my ($self) = shift;
>     my ( $relatives, $params ) = @_;
>     my @params  = @{$params};
>     my $Aligner = new
> Bio::Tools::Run::Alignment::TCoffee(@params);
>     my $aln     = $Aligner->align($relatives);
>
>     return $aln;
> }
>
> I don't really have time to swap the program I'm
> using, so I hope I can get this to work!
>
> Thanks again- help appreciated.
>
> Jon
>
>
>  --- Jason Stajich <jason at cgt.duhs.duke.edu> wrote:
>> different versions of bioperl/bioperl-run on the dev
>> machine and other
>> machine?  This happens for every every
>> alignment you try on the non-dev machine? i.e.
>> % perl -I. -w t/TCoffee.t
>> in bioperl-run fails on the new machine too?
>>
>> An example sequence file and the script with at
>> least the t-coffee part
>> would help in debugging the problem if all of that
>> is true.
>>
>> I've also moved to using MUSCLE instead of T-Coffee
>> for some analyses
>> because it is much faster and seems to be as
>> accurate.  The newest MAFFT
>> is also rumoured to be as accurate too although one
>> should always do their
>> own tests on one's own data first...
>>
>> -jason
>> On Fri, 27 Aug 2004, [iso-8859-1] Jonathan Manning
>> wrote:
>>
>>> Hi to all,
>>>
>>> I've been using T-Coffee via the Bioperl wrapper
>> as
>>> part of a larger project. Though it worked fine on
>> the
>>> development system, it's not working on a
>> different
>>> one. It seems to do the pairwise stuff, at least
>> it
>>> gets to this stage:
>>>
>>> ......
>>> 	AAH76853  CAG05593 : score=  400
>>> 	AAH76853  CAE45989 : score=  410
>>> 	CAG05593  CAE45989 : score=  460
>>>
>>>
>>> MAKE NEIGHBOR JOINING DENDROGRAM
>>> 	[MODE=fast] [Output dendrogram
>> file=5XIMxfCi1F.dnd]
>>>
>>>
>>> But then it crashes out with the following
>> messages:
>>>
>>> Abnormal Program Termination:[T-COFFEE,
>> Version_1.37]
>>> Please report the fault to:
>>> cedric.notredame at europe.com (Indicate the version
>>> number)
>>> Thank you for your cooperation :-)
>>>
>>> ------------- EXCEPTION  -------------
>>> MSG: TCoffee call crashed: 256 [command
>>> /usr/bin/t_coffee
>>>
>>
> -in=/tmp/5XIMxfCi1F,XBLOSUM,Mlalign_id_pair,Mclustalw_pair
>>>  -ktuple=2 -output=clustalw
>>> -outfile=/tmp/6wIuLkvcGl/w7jE5bLbih]
>>>
>>> STACK Bio::Tools::Run::Alignment::TCoffee::_run
>>>
>>
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:814
>>> STACK Bio::Tools::Run::Alignment::TCoffee::align
>>>
>>
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:719
>>> STACK SSIR::align
>>> /usr/lib/perl5/site_perl/5.8.0/SSIR.pm:2094
>>> STACK toplevel /var/www/cgi-bin/ssir.cgi:557
>>>
>>> --------------------------------------
>>>
>>> Similar commands work fine from the command line.
>>>
>>> Does anyone have any ideas?
>>>
>>> Many thanks,
>>>
>>> Jon
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
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>>
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>>>
>>
>> --
>> Jason Stajich
>> Duke University
>> jason at cgt.mc.duke.edu
>>
>
>
> 	
> 	
> 		
> ___________________________________________________________ALL-NEW 
> Yahoo! Messenger - all new features - even more fun!  
> http://uk.messenger.yahoo.comXP_058513 PREDICTED: similar to RIKEN 
> cDNA 4921513O20; cDNA sequence, clone 3-75 [Homo sapiens].
> MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNI
> HVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILK
> MLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLG
> CKALHVLFERGNNVEVLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNI
> LVLNEVHEFVVKAVQQYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEED
> KLFWLEACYKALTWHRKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSM
> LMHSSSKEVFQASANALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKM
> LNHLFEGSNTSLDIMAAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTE
> FHHKLNMVKKQCFKNDIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGA
> MDSVLHTLQMYPDDQEIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQ
> TKGFQTILAILKLSASFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMD
> DYLKNVMLERACDQNNSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSG
> SREQDVRKALTISIGKGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDK
> TSNLRKQTNIASTLARMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDS
> VFAQSDDLDSEGSEGSFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDL
> LKRKRKILSSDDSLRSSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCC
> ISVHLEHLEKLELHQNALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDV
> SRNDIGPSVVLDPTVKCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSP
> LRLKELKILNLSKNHISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKF
> SCIPEAILNLPHLRSLDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWS
> RVEKLHLSHNKLKEIPPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLN
> FDFKHIGCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQ
> SATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQ
> AEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDY
> HFVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEF
> PVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCK
> IMAQILTVKVEGCPKHPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEE
> YLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRER
> ALRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHID
> SLMEEWFPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQ
> PRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAV
> KIFNKHTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKAS
> LTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCC
> RMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDE
> LEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRIL
> LPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALV
> HLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLV
> GTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFS
> FSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCG
> LIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLI
> RVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQ
> NLEKHIEVRKELAEKMRRTSVE
>> CAD39185 hypothetical protein [Homo sapiens].
> VFDILNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTE
> GYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTC
> LYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSEST
> NSTERNVMWGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAK
> QNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWI
> GTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQK
> EIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE
>> BAB29628 unnamed protein product [Mus musculus].
> MLGAIFERPIPPDTRPWYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCR
> MGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLHDIWTTGSRIMEGLRFPNEFDEL
> AIQGKLPDPVKEYGCAPWPMVEKLITKCLKENPQERPTSAQVFDILNSAELICLMRHILI
> PKNIIVECMVATNLNSKSATLWLGCGNTEKGQLSLFDLNTERYSYEEVADSRILCLALVH
> LAAEKESWVVCGTQSGALLVINVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQSNFLLVG
> TADGNLMIFEDKAVKCKGAAPLKTLHIGDVSTPLMCLSESLNSSERHITWGGCGTKVFSF
> SNDFTIQKLIETKTNQLFSYAAFSDSNIIALAVDTALYIAKKNSPVVEVWDKKTEKLCEL
> IDCVHFLKEVMVKLNKESKHQLSYSGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIR
> TIHNFCDSVRAMATAQLGSLKNVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNLPHEVQN
> LEKHIEVRTELADKMRKTSVE
>> AAH34074 4921513O20Rik protein [Mus musculus].
> SEIIIRLYEMPYFPMGFWSRLINRLLEISPFMLSGRERALRPNRMYWRQGIYLNWSPEAY
> CLVGSEVLDNRPESFLKITVPSCRKGCILLGRVVDHIDSLMEEWFPGLLEIDICGEGETL
> LKKWALYSFNDGEEHQKILLDELMKKAEEGDLLINPDQPRLTIPISQIAPDLILADLPRN
> IMLNNDELEFEEAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHL
> HHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYLHS
> AMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGN
> VIYNQQADVYSFGLLLHDIWTTGSRIMEGLRFPNEFDELAIQGKLPDPVKEYGCAPWPMV
> EKLITKCLKENPQERPTSAQVFDILNSAELICLMRHILIPKNIIVECMVATNLNSKSATL
> WLGCGNTEKGQLSLFDLNTERYSYEEVADSRILCLALVHLAAEKESWVVCGTQSGALLVI
> NVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQSNFLLVGTADGNLMIFEDKAVKCKGAAP
> LKTLHIGDVSTPLMCLSESLNSSERHITWGGCGTKVFSFSNDFTIQKLIETKTNQLFSYA
> AFSDSNIIALAVDTALYIAKKNSPVVEVWDKKTEKLCELIDCVHFLKEVMVKLNKESKHQ
> LSYSGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIRTIHNFCDSVRAMATAQLGSLK
> NVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNLPHEVQNLEKHIEVRTELADKMRKTSVE
>> XP_235581 similar to RIKEN cDNA 4921513O20; cDNA sequence, clone 3-75 
>> [Rattus norvegicus].
> MASGACQGCDEEEEEEALKKLIVRLNNVQEGKQIETLLQLLEDILVFTYSDRASKLFEGK
> NVHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTLQSLIGPQDIGNDWEVLGIHRLI
> LKMLTVHHANVNLSIVGLKALDLLLDSGKITLLILDEECDVFLLIFDAMHRYSANEEVQK
> LACKALHVLFERVSEEQLTEFVENKDYMTLLSTFRSFKRDEEIVHHVLCCLHSLAVTCSN
> VEVLMSGNVRCYNIVVEAMKTFPTSENIQEVSCSLLHKLTLGNFFNILVLNEVHVFVVKA
> VQRYPENVALQISALSCLALLNLEERSETQENSDEDSEKPFWLEPCYKALMRHRKNKHVQ
> EAACWALNNLLMYQSSLHEKIGDEDGQFPAHREVMLSMLMHSSSKDVFQAAAHALSTLLE
> QNGLPLASIINGGMACICTHKVSLVHAPMSSILVLPSSMKILLAKGVYLNVLELMQRHAQ
> VPEVAESGCKMLSHLFEGSNPSLDTVAAVIPKILTVMRTHGTSLSVQLEALRALLHFVVP
> GVSEDSRDDSRCQPNVLRTQCFRTDIHKLVLAALNRFIGNPGIQKCGLKVISSFAHLPDA
> LEMLSLHGAVDSVLHTLQMYPDDQEIQCLGLHLMGCLMTKKNFCIGTGHLLAKILASTLQ
> RFKDVAEVQTTGLQTVLSMLDLSVSFSKLLVHYSFDVVMFHQMSSGVLEQKDEQFLNLCC
> KCFAKVAVDDELKSKMLERACDQNNSIMVECLLLLGADANQAKGATSLIYQVCEKESSPK
> LVELLLNSGCREQDVRKALTVSIQKGDNQVISLLLRRLALDLANNSICLGGFCIGKLDPS
> WLGPLFPDKSSNLRKQTNAGSVLARKVLRYQMRNTLQEGVASGSEGNFSEDALAKFGEWT
> FIPDSSMDSVFGQSDDLDSEGSESSFLVKKKSNSVSVGEVYRDLALQRCSPNAQRHSSSL
> GPVFDHEDLLRRKRKILSSDESLRSSRLQSHTRQSDSSSSLASEREHITSLDLSANELKD
> IDALGQKCCLSSHLEHLTKLELHQNSLTSFPQQLCETLKCLTHLDLHSNKFATFPSFMLK
> MPSVIHLDASRNDIGPTVVLDPVVKCPSLKQFNLSYNQLSSIPENLDQVVEKLEQLLLEG
> NKISGICSPLSLKELKILNLSKNHIPSLPEDFLEACPKVESFSARMNFLAVHTVSLPPTG
> FILVCFVKIPPEIGRLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDGLHLNFDFKHI
> GCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKMKKSELGMQGATVGI
> DVRDWPIQIRGKRKKDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAM
> KPWLFNIKARASSSPVILVGTHLDVSDEKQRKACIGKITKELLNKRGFPTIRDYHFVNAT
> EESDALAKLRKTIINESLNFKIRDQPVVGQLIPDCYVELEKIILSERKAVPTEFPVINRK
> HLLQLVKEHQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKVMAQIL
> TVKVDGCLKHPKGIISRRDVEKFLSKKKRFPKNYMAQYFKLLEKFQIALPIGEEYLLVPS
> SLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPFMLSGRERALRPNR
> MYWRQGIYLNWSPEAYCLVGSEVLDSRPESFLKITVPSCRKGCILLGRVVDHIDSLMEEW
> FPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDELMKKAEEGDLLINPDQPRLTIP
> ISQIAPDLILADLPRNIMLNNDELEFEEAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKH
> TSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQ
> HRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKT
> SEGTPGFRAPEVARGNVIYNQQADVYSFGLLLHDIWTTGNRIMEGLRFPNEFDELAIQGK
> LPDPVKEYGCAPWPMVEKLITKCLKENPQERPTSAQVFDILNSAELICLMRHIFIPKDIT
> VECIAATNLNSKRATLWLGCGNTEKGQLSLLDLNTERYSYEEVTDSRILCLALVHLAAEK
> ESWVVCGTQSGALLVINAEDETRRHTLDKMTDSVTCLYCNSFAKQSKQSHFLLVGTADGN
> LMIFEDKTIKCKGAAPLKTLHIGDVSTPLMCLSESMNSSERHITWGGCGTKIFSFSNDFT
> IQKLIETRTNQLFSYSAFSDSNIIAVAVDTALYIAKKNSPVVENYKSCDAGDRSQATCVQ
> NSEMTTALPPSCFKVLAGCTRLGRSVKSLSADRTVNEHILYASREVMVKINKDSKHKLSY
> SGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIRTIHNFCDSKLSMFCFGKGSLKNVM
> LVLGYKRKSTEGTQEQKEIQSCLSIWDLNLPHEVQNLEKHIEVRTELADKMRKTSVE
>> AAH35949 4921513O20Rik protein [Mus musculus].
> CLALVHLAAEKESWVVCGTQSGALLVINVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQS
> NFLLVGTADGNLMIFEDKAVKCKGAAPLKTLHIGDVSTPLMCLSESLNSSERHITWGGCG
> TKVFSFSNDFTIQKLIETKTNQLFSYAAFSDSNIIALAVDTALYIAKKNSPVVEVWDKKT
> EKLCELIDCVHFLKEVMVKLNKESKHQLSYSGRVKALCLQKNTALWIGTGGGHILLLDLS
> TRRVIRTIHNFCDSVRAMATAQLGSLKNVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNL
> PHEVQNLEKHIEVRTELADKMRKTSVE
>> XP_415940 PREDICTED: similar to hypothetical protein [Gallus gallus].
> MKVYEILNSAELICLMRYVSIPSTSTAECMVAANQSCKKAGVWIGNGNTEKAQLSFVNLN
> TDGHTCEDIADSKILSLALVTLPTEKENWIVAGTHSGSLWAVNTEDETRRHRLQKMSDSV
> TCLYCNSLSKQSKQKNFFLVGTADGTLAVFEDRAVKCKGATPLKILTIGNVSTPLMCLNE
> STYLSEKNTIWGGCGTKLIALSSDFSVQKLIETKSSQLFCHNAYSDANIISIAVDKSIYL
> AKKNSHFVEIWDKKTEKLSELIDCAHFLKDEVEKLNKESKHKVAYSGRVKTICLQKNTAL
> WVGTGGGHILLLDLSTRRPVRVIDNFCDSIRVMLTAQLGSLKNVVLVLGYCYKSDTEDDK
> SHKELQSCVSVWDINLPHEVQNLKKHIEHSYNTATARIALWPRTGPGSPCPVTGRSDRAH
> SSSPAHTAMAESHRAAHREPCYVSAGPAAFLYLGISAVTWKASVCPRHPQLLQHSKLKRY
> TTGAKASAQNNVGWAPFSSQSRADVSPSHPDQTSQEGAFGGEPEAHPLPAALLGQQAALF
> PPHLNAVAAALCQQLVAVQSMLSNCIARFLSNCAGYLELSSTQQPLKSLQRSPQGIGEWG
> GAPSPGHSQTHHSSSQHDCKLPPEHSAKAGTAAVGP
>> AAH76853 Unknown (protein for IMAGE:6637919) [Xenopus laevis].
> IAPDIVLADLPRNIMLNAEELEFDQAPEFLLGDGGFGSVYRASYKGEDVAVKIFNKHTSS
> RLLRQELTVLSHLHHPSLVYLLAAGVHPRMLVMELAPKGSLDHLLQQDSASLTRTLQHRI
> ALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNSAIIAKIADYGIAQYCCRMGIKTSEG
> TPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTGGARMVEGLKFPNEFDELAIHGRLPD
> PVKEYNCAPWPEVEVLIKKCLKENPQQRPTSVTVYEILNSAELLCLMRNHVIFSMLTAEC
> MVAASPLVKKHVVWVGNGCTEKGQMCCIDLNKGGQTCEDFSDSRILCLTLVTLPGEKQNW
> IVAGTQSGEIITADLDELKIKHTLHKLTDSVTCLLFSCIQGQSQKKYHILAGTANGRIAI
> FENTAVKCAYAAPIKVIDIGDNSTPVMCLCESTYSSEKNSVWGICGTKIFSLSSEFTVQK
> TIDTRTATLYSHGSYSESNITCFAIDKYIYVAKKISPYVEIWDKKTEKICEVLDCVQFLK
> EDSRKRRKCKQEEAYTSRVKALYLQKNTALWVGTGGGHILLIDLSTRQPIRIITSFCDSI
> RSMVPAQLDRGSIKNVVLVLGCRCTPQKEIQSFLSVWDTNLPHEVQNLKKHNEIRQEFAD
> KLRGLSMD
>> CAG05593 unnamed protein product [Tetraodon nigroviridis].
> MVNGEELEEQLRKLLVRLKSQQQERQLGTLIQILQDLLFLAHTDEAAELFEDKDVHVSLT
> VALSSYASRRGVQQVGWSLLCRLMEICPGTLERLTAAQPAAEDSQVLPVHKLVLKVLSQH
> GADCKVTMVGLRALALLLRSDAVPPLLLEDESEDVLGLVVQAMKVFPVNEEVLLHGCGAL
> QVLLETVSEDHLVEFVENQDHVVVLAALQTFLDNPELLLRGLKVLLPLARPGGVRCYSTV
> IAAMDAFPEVEDLQETACRLFRAFTLESYYNILVRNGVQRVAACCTALDLHAEEPDVQEA
> ASWAIERLLVHGAGPRPAEEDQEERTPVHRQLMAALLLHPKAPSVFQAATSAISTLIQQD
> GERSTPRAAVKRCLVPPTFAAFAGRTRAPLLSSGLHVNLVEMMKRHWTSAEVSISACRLL
> SLLFQGRPASLDELNMTMSQILCTIKAHNFNPEVQLEALRASLVLLYPDRSLREHGVSVA
> DPDMADVSLKVLKNQCVLEGAHTLYLEVLNRFISSSAIQKSGLKVLSALADCSGAVDLLC
> QQGAIDTVLHTLQMFPGEREIHYWGFTLLNYLVTKKKLSPMIVPVLASVLVASLVQYRED
> SEMTLKCFQVALRMLDASPRSAAELQRENFDRQIFQQLREDTADLCNYPLRKSVCLALFK
> MWSDSELRYAMLEKACQDGDATMAECLIELGADVNAKTKSESLLYQVGGENLCVHRSVLT
> AGPSVPQVCERGGPLELAELLVRRGAHEQHLRRALAVSVKRADGPAVILLLARLGLDHNS
> SALCLGGFRLGRLDAGWLGPLLAERRSARSLCRTSSKAVSLARFVQSFQRSKSHSSVLRS
> PVDPCLTSGYISEESDDSNFSFVSVDDGQIPNEDMESDGSDSLPGVLSPEDPQALRRRQG
> RQRHPSPEVQPPHQRPGCVGVFFSLFAPVFVFLFQNGQTETEPCDSVQKRYAKSPQKVFR
> PADGPAALQKVQDRVRLLDLSANELDALSCLMDDGVVQQQLGHLLRLDLSHNSLQEFPSS
> LCQSLSSLTRLDLQGNQLPSLPVELLTLQSLNTLNISRNCVGPQLTFDPAVSCPSLRHLN
> LSFNKIAAFPHQLSGAGSQLEELCLEGNCIRELCVPLSLPEIKLLDVSKNSVETVSADFL
> TGCPKLETLNVSVNKISSLSHLPSKLTTLKLANNGFAEVSAAILGLPNLRSVDMRTNRIA
> ALPGPASWESCNLRELNFSQNRIGTLDLSGPVHRWARLEKLHLSDNQLSEIPPQIGLLEG
> LNSLDVSRNANLHSFPDEMGKLGRLWDLPLDGLRLQLDLKLIGNKTKDIVRFLQQRLKKA
> VPYHRMKLIVVGNVASGKTTLIQQLMKLKRSQLKSKSTSVGIDVQDWTIKDWDRKKMVLN
> VWDFSGGEEFSGSHPHFLTSRALYLVVYNLSRGASQVDALKPWLFNIKAAAPVSPVILVG
> THTDVSNELQLQACLTKIREELLSHQSFPAIRDYHMVSASEDSDALTKLRKAIAREVANF
> KIQGQPVMGQLVPDSYVELERQLLQERARVPPEFPVLRHREVLQLIQENQLQLEEAELPH
> AIHFLSEAGQNFHELFFPLLTVLSDFLDFRSGNVELRSCSEEGRLYSHLLVFPAGVLLHF
> DDPALQLQNLYFIDPQWLCHIISQKLTLKSCGFWEPPKGVIQRSLVEKFLSETKCFPKSH
> MTQLFKLLEKFQIALPFGEDQLLVPSRWAHGRSVQRQHTAVCVFVSVGNPTDVGSVFGPS
> LSKHRPVIELPHGENSEVIVRLYEMPYFPMDFWSRQIIRLLEFSSHLLSGREKAVRPNRI
> YWRRGVYLSWSPDAYCLVEAASVEDNPSSFVRITVPSSQKGRVLLGQVVDHVDSLLEEWF
> PGLLSTNMHGSGEALLKKWALYSFEDGQEWSKVLLDDLCPHLDAGVLLQDEEQPGLALPL
> SQVAPDLVLSDQPAGLMLDSAELSVDLSERLGTPATRPEPRLGVLLSDNVLFPGGGGFGN
> VYRGVYRKEDVAVKIFNNHASELYVFRLLRQELVVLSRLRHPSLVALLAASTAARALVME
> LAPRGSLDALFQHENGGLNRKLQHRIALQVADGLRYLHSAMIVYRDLKPHNVLLFNLKTD
> CEMIAKITDYGIAQHCCSMGVRSCEGTPGGLSSWAWFCSRFLPVQRQFVLGVQALGFRLC
> KAPGGERRVVDGCASAGFRAPEVARGNVAYNQQADVFSFGLLLYDLLTCGERISDGMKFP
> SEFDEIAVQRKLPDPVKHYGCAPWPGLQALMRDCLKESPQCRPTSAQVFDRLNSGEVLCL
> MRELAVPRVPSAECLALSGGCTAWLGGGSSAQRRGSVTAVNLHTNAVTTEAIDTSPVLCL
> TTVQIPNQTSDWLVAGTQSGALVVLSSQDALTWHRLQSVRDAVTSLFFHLHPCRNQRKNY
> LLVGTADGTVTIYEDSVLKQEDGRPVKTVTVGQLDTPVVCLGQSLHWQDSRCVWAGCGTK
> VLSFTADYDLGRSVDTRPSAEFQQEQSWASEACVSRMVVDKHVYLSKAGSPLVEVWDKKS
> ERMVDRIDCAHIIRRDSGGTTEGSSSWARVKALLVQSAAALWIGTRGGYLLLLELSKHQP
> LQVIGPRCDSVRCMAPALIETPNWKNVVLVLGRRLPQGRNQADEESVLMVWNGMLPMEAK
> DLKRHCHRREQVAVRMR
>> CAE45989 hypothetical protein [Homo sapiens].
> TEKLCGLIDCVHFLREVTVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDL
> STRRLIRVIYNFCNSVRVMMTAQLGKFLSFRYFSYSLSLIKYAFILRLHFL
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/