Hi !!
in my tests using emboss apps in Taverna I tried to bootstrap my alignment
to obtain a phylogenetic tree. I used fseqboot to perform the
bootstrapping for my proteins in this manner :
alignments -> fseqboot -> fprotdist -> fneighbor
but it fails and returns a message like this :
ERROR 2009-05-05 10:43:02,125 Failure while executing task fneighbor
uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException:
Soapla
b call returned an error : Summary:
Completed: Erroneously
Termination status: 139
Started: 2009-May-05 09:42:24 (BST)
Ended: 2009-May-05 09:42:25 (BST)
Duration: 0:00:00.411
Report:
Some error messages were reported.
Name: phylogeny_distance_matrix.fneighbor
Job ID: phylogeny_distance_matrix.fneighbor_7cb923b5.120e2d551e0._7f3e
Program and parameters:
/ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor
-datafile
/ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f
neighbor_7cb923b5.120e2d551e0._7f3e/i_datafile
-treetype
n
-outfile
/ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f
neighbor_7cb923b5.120e2d551e0._7f3e/o_outfile
-outtreefile
/ebi/extserv/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.f
neighbor_7cb923b5.120e2d551e0._7f3e/o_outtreefiletreefile
-auto
--- end of parameters
Exit code: 139
Standard error stream:
/homes/tc_user/.lsbatch/1241512944.708672: line 8: 14611 Segmentation fault
(core dumped) /ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor -datafile
/ebi/extser
v/soaplab-work/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.fneighbor_7c
b923b5.120e2d551e0._7f3e/i_datafile -treetype n -outfile
/ebi/extserv/soaplab-wo
rk/tc-soaplab-emboss4/SANDBOX/phylogeny_distance_matrix.fneighbor_7cb923b5.120e2
d551e0._7f3e/o_outfile -outtreefile
/ebi/extserv/soaplab-work/tc-soaplab-emboss4
/SANDBOX/phylogeny_distance_matrix.fneighbor_7cb923b5.120e2d551e0._7f3e/o_outtre
efiletreefile -auto
in attach there are the input file and the workflow I used.
Could you tell me where is my error?!
thank you
regards
(I'll try to send you a sample of my other apps faults later)
Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA.
Come fare:
Nella prossima dichiarazione dei redditi metti la firma
nell'apposito riquadro del 5 per mille,
scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul
Cancro di Genova :
c.f. 80 100 850 108
Istituto Nazionale per la Ricerca sul Cancro
L.go R. Benzi, 10 -16132 Genova
http://www.istge.it
<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"; version="0.2" log="0">
<s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:1284a957-6ffd-4c8b-b0a9-2b90697d1427" author="Mariana de Oliveira Braga Teixeira Monteiro" title="EMBOSS NJ Tree">This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.</s:workflowdescription>
<s:processor name="fdrawtree">
<s:description>Plots an unrooted tree diagram</s:description>
<s:soaplabwsdl interval="60000" backoff="1.1" maxinterval="60000">http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_tree_drawing.fdrawtree</s:soaplabwsdl>
</s:processor>
<s:processor name="fprotdist">
<s:description>Protein distance algorithm</s:description>
<s:soaplabwsdl interval="60000" backoff="1.1" maxinterval="60000">http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fprotdist</s:soaplabwsdl>
</s:processor>
<s:processor name="fdrawgram">
<s:description>Plots a cladogram- or phenogram-like rooted
tree diagram</s:description>
<s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_tree_drawing.fdrawgram</s:soaplabwsdl>
</s:processor>
<s:processor name="fneighbor">
<s:description>Phylogenies from distance matrix by N-J or
UPGMA method</s:description>
<s:defaults>
<s:default name="treetype">n</s:default>
</s:defaults>
<s:soaplabwsdl interval="60000" backoff="1.1" maxinterval="60000">http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_distance_matrix.fneighbor</s:soaplabwsdl>
</s:processor>
<s:processor name="fconsense">
<s:description>Majority-rule and strict consensus tree</s:description>
<s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_consensus.fconsense</s:soaplabwsdl>
</s:processor>
<s:processor name="fseqboot">
<s:description>Bootstrapped sequences algorithm</s:description>
<s:defaults>
<s:default name="sprotein_sequence">yes</s:default>
<s:default name="snucleotide_sequence">no</s:default>
<s:default name="seqtype">p</s:default>
<s:default name="progress">no</s:default>
</s:defaults>
<s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fseqboot</s:soaplabwsdl>
</s:processor>
<s:link source="Alignments" sink="fseqboot:sequence_direct_data" />
<s:link source="fconsense:outtreefile" sink="njtree" />
<s:link source="fneighbor:outtreefile" sink="fconsense:intreefile_direct_data" />
<s:link source="fseqboot:outfile" sink="fprotdist:sequence_direct_data" />
<s:link source="fdrawgram:plotfile" sink="Rooted" />
<s:link source="fdrawtree:plotfile" sink="Unrooted" />
<s:link source="fneighbor:outfile" sink="Distance" />
<s:link source="fneighbor:outtreefile" sink="NJ" />
<s:link source="fneighbor:outtreefile" sink="fdrawgram:intreefile_direct_data" />
<s:link source="fneighbor:outtreefile" sink="fdrawtree:intreefile_direct_data" />
<s:link source="fprotdist:outfile" sink="fneighbor:datafile_direct_data" />
<s:source name="Alignments">
<s:metadata>
<s:description>Enter a novel protein sequence. e.g.
AITRRVACLDGVNTATNAACCALFAVRDDIQQNL
FDGGECGEEVHESLRLTFHDAIGISPSLAATGKFGG
GGADGSIMIFDDIEPNFHANNGVDEIINAQKPFVAK
HNMTAGDFIQFAGAVGVSNCPGAPQLSFFLGRPA</s:description>
</s:metadata>
</s:source>
<s:sink name="NJ" />
<s:sink name="Distance" />
<s:sink name="Rooted" />
<s:sink name="Unrooted" />
<s:sink name="njtree" />
</s:scufl>
>gi|186968859|gb|ACC97187.1| piwi protein WI-3 [Schmidtea mediterranea]
------------------------------------------------------------
------------------------------MSGSSGIGRGRSRGLLMQKFLNKDVLVPSV
ESLEDKALNKLGIPPPGSTVEKNTESSSISSGDSRSNPSGDSRNNIKLQDSDIENRNI--
------------------------------------------------------------
-----------------------------------------------------TIVTRPL
SCIGRGRGLSNPSSLTTSSGKSDKITENEEPGQIKKFVGRGRGLLNSQKECSNSTPSEVS
NELKQMKISNDDKMTVSSEAKSQFENIEKPISKFRRREYPTQIKEPCNTRNDSSPSLTLS
ANYVKVRTTQPHIYQYHVSFAPPIDSRLMRIKIVQGLSESDLGVVKEARAFDGMNLYIPQ
LLKNKETIIKVNKPTDKTVVDVKVVFTNNVNFSECPMVYNVLFKRIENSLRMVKIGRDYF
YPEKKIVLDRRRMEIWPGYVTSIQNFDGGLLLQCDVSHKVIRNDSVYDIMMEINKTVNNK
GQMQTAAINQLLGQIVLTPHNNRNYRITDIDWAKN-CLSEFDKGGE--KISYRDYFRNTY
GLQIRDLEQPMIVSKSNSRSGKNR-GPKGSKEVDGGLVYLIPELCMLTGLTDDMIKDFRL
MRELHEHC----RVTPKKRHEALLEFVDNIYSCEEAKKLLGYWGITIEKDTVNINACKMN
PEMIYFGNEASV--SAGEQAEF--KQALA--HNKVIGGIRIENWILISPKSLLTKANGLL
QALMSKSP----RVGVMFGKPKIVEMNNDRTEEYLK--------ELKRNVAPGVQLVVTI
LS-------------AVREDRYNAIKKFCYVDCPVPSQVVLAQTLKEGPKLNSVAVNIAL
QINAKLGGELWAVKIPIKKFMVVGLDVWHDTKGRSRSVGAVVGSTNALCTRWFSKSHLQE
QDKEIMYVLQSCMLSLLKAYFEENNFLPETIFMYRDGVSDGQLGYVQKTEIEQFFKVFES
FSADYKPNM---------------------------------------------------
----------------------------------------VYNVVQKRINTRLYVSDPKN
KGQINNPNPGTIVDHTVTR-----ANLYDFFLVSQSVRQGTVTPTHYVVLCDNSKYTPHQ
VQLMAYKTCHIYYNWPGTVRVPAPCMYAHKLAYMVGQNLKAEPSNLLCDRLFYL
>gi|18398572|ref|NP_565429.1| WUS (WUSCHEL); DNA binding / transcription factor
>[Arabidopsis thaliana]
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
---------------------MEPPQH---------------------------------
------------------------------------------------------------
--------------QHHHHQADQESGNNNNNKSGS-GGYTCRQTST--RW----------
---------------------------------------------------TPTTEQIKI
LKELYYNN----AIRSPTADQIQKITARLRQ------------------------FGKIE
GKNVFYWFQNHK-------ARE--RQKKRFNGTNMTTPSSSPNSVMMAANDHYHPLLHHH
HGVPMQRPANSVNVKLNQDHHLYHHNKPYPSF------------NNGNLNHASSGTECGV
VN-------------ASNGYMSSHVYGSMEQDCSMNYNNVGGGWANMDHH----------
----------------------------------------------------YSSAPYNF
FDRAKPLFGLEGHQEEEECG--GDAYLEHRRTL---------------------------
------------------------------------------------------------
----------------------------------------PLFPMHGEDH----------
----INGGSGAIWKYGQSE-----------------------------------------
----------------------------------VR------PCASLELRLN--
>gi|30681653|ref|NP_187735.2| WOX5 (WUSCHEL-related homeobox 5); transcription
>factor [Arabidopsis thaliana]
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
--------------MSFSVKGRSLRGNNNG---------GTGTKCG--RW----------
---------------------------------------------------NPTVEQLKI
LTDLF-RA----GLRTPTTDQIQKISTELSF------------------------YGKIE
SKNVFYWFQNHK-------ARE--RQKRR---------------------KISIDFDHHH
HQPSTRD-----------------------------------------------------
------------------------VFEISEEDCQEEEKVIETLQL---------------
----------------------------------------------------FPVNSFED
SNSKVDKMRARGNN----------------------------------------------
------------------------------------------------------------
----------------------------------------QYREYIRETT----------
------TTSFSPYSSCGAE-----------------------------------------
----------------------------------ME------HPPPLDLRLSFL
>gi|85376478|gb|ABC70476.1| bruno-like [Schmidtea mediterranea]
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
--------------------------------------------MQVASPINVDSMALYS
NGFTDKGNIIIQNHDENTKLFIGM------------------------------------
------------------------------------------------------------
---------------------LNKNQS---------------------------------
------------------------------------------------------------
--------------EDDVRQLCEPYGCIKNCMILK-DSYGNSKGCAFVTYNNSDEANMAI
ESLNGMKTSMACPELGSCIVARLADNEQERQLRKMQMQ-------------FPAIQLLTP
QNVGYYNQ----GIVPMILQQFPHATDQQTANL-------------INAYALQMHLSQMY
SPNLTPPLVNSSPSVTPQPQIG---VPMSAANDISSNQCSMNHFVLPSINNENIPLSPAL
NSYINPAHPQLINIANINFTPEALHLPS----------------LYSMFPQCGFNLNTPA
LG-----------LSGQNIYPNTTALSLQYQQNQKDGIKDNIVTGPEGCNLF--------
----------------------------------------------------IYHLPQDF
GDAALAQLFTPFGNVISAKVYLDRATNQSKC-----------------------------
------------------------------------------------------------
----------------------------------------FGFVSFDNASNAEAAIRGMN
GFQIGTKRLKVQLKRPKGE-----------------------------------------
------------------------------------------------YKN---
>gi|75265949|sp|Q9SJJ3.1|BLH8_ARATH RecName: Full=BEL1-like homeodomain protein
>8; Short=BEL1-like protein 8; AltName: Full=Protein POUND-FOOLISH
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------------------------------------------MDMIKPD
FQQIRRDKFRVEQMNDFPNTWTQQQHQNIRIPNNLDLIGILQNQISVPVQTDLYQDSAAT
FMN---------------------------------------------------------
---------------------MPQSIH---------------------------RDPQGP
SNWRISDLSQPSTVNHGYDQAGIRPNNVADLLSDHFSSRNQILDRPLYVGRDSIPQSSMI
RRSEVSCL------DDNQKGCVTVACSGTGNEILR-SSYDQGSSSG--SY----RGEFSF
LPSLENQSVAHNASNWNHGPVNVTATSHTNSKKGFPLSLLSDIPPSRDVGNAAVLSTMNI
HGPLGPFT----GYASILKSSRFLEPAQKMLEEFCISY----ASKIISRSESTSMEDDDD
DDDNLSGFSSSSEPLEPKNRLK--KAKLLFLQEEVCKWYKLYNHQLQTVMSSFNTVAGLN
TATPYI------SLALKRTSRSFKALRTA-----------IAEHVKQISSHSSNGNNNNR
FQ------KRQRSLIGNNVGFESQQQHIWRPQRGLPERAVAVLRA---------------
--------------------------------------------------WLFDHFLHPY
PTDSDKQMLATQTGLSRNQV--SNWFINARVRLWKPMVEEIHTLETKAIKNADTSHNIEP
------------------------------------------------------------
----------------------------------------SNRPNTVSSPSHEQTLTGLS
GTKRSRLEYMDMVGFNRGN-----------------------------------------
-----------VSLTLELRRGVDNVIQTQTQDHQFG-------TGSQMFHDFVG
>gi|75264476|sp|Q9LZM8.1|BLH9_ARATH RecName: Full=BEL1-like homeodomain protein
>9; Short=BEL1-like protein 9; AltName: Full=Protein BELLRINGER; AltName:
>Full=Protein LARSON; AltName: Full=Protein PENNYWISE; AltName: Full=Protein
>REPLUMLESS; AltName: Full=Protein VAAMANA
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----------------------------------------------------------MA
DAYEPYHVLQQSRRDKLRIPSLDSHFHFHP------------------------------
------------------------------------------------------------
---------------------PPPPSS---------------------------------
--------------------------------------GGGGGVFPLADSDFLAAGGFHS
NNNNNHISNPSYSNFMGFLGGPSSSSSTAVAVAGD-HSFNAGLSSG--DVLVFKPEPLSL
SLSSHPRLAYDLVVPGVVNSGFCRSAGEANA--------------------AAVTIASRS
SGPLGPFT----GYASILKGSRFLKPAQMLLDEFCNVGRGIYTDKVIDDDDSSLLFD---
--PTVENLCGVSDGGGGDNGKK--KSKLISMLDEVYKRYKQYYEQLQAVMGSFECVAGLG
HAAPYA------NLALKALSKHFKCLKNAITDQLQFSHNNKIQQQQQCGHPMNSENKTDS
LRFGGSDSSRGLCSAGQRHGFPDHHAPVWRPHRGLPERAVTVLRA---------------
--------------------------------------------------WLFDHFLHPY
PTDTDKLMLAKQTGLSRNQV--SNWFINARVRVWKPMVEEIHMLETRQSQRSSSSSWRDE
RTSTTVFPDNSNNN----------------------------------------------
----------------------------------------PSSSSAQQRPNNSSPPRRAR
NDDVHGTNNNNSYVNSGSGGGSAVGFSYGIGSSNVPVMNSSTNGGVSLTLGLHHQIGLPE
PFPMTTAQRFGLDGGSGDGGGGYEGQNRQFGRDFIG------GSNHQFLHDFVG
>gi|1170676|sp|P46639.1|KNAT1_ARATH RecName: Full=Homeobox protein
>knotted-1-like 1; AltName: Full=Protein KNAT1; AltName: Full=Protein
>BREVIPEDICELLUS
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------------------------------------------------M
EEYQHDNSTTPQRVSFLY------------------------------------------
------------------------------------------------------------
---------------------SPISSS---------------------------------
------------------------------------------------------------
--------------NKNDNTSDTNNNNNNNNSSNYGPGYNNTNNNN--HHHQHMLFPHMS
SLLPQTTENCFRSDHDQPNNNNNPSVKS-----------------------EASSSRINH
YSMLMRAIHNTQEANNNNNDNVSDVEAMKAKIIAHPHY--------STLLQAYLDCQKIG
APPDV--VDRIT--AARQDFEA--RQQRSTPSVSASSRDPELDQFMEAYCDMLVKYREEL
TRPIQEAME---FIRRIESQLSMLCQSP----------------IHILNNPDGKSDNMGS
SD-------------EEQENNSGGETELPEIDPRAEDRELKNHLLKKYSGYLSSLKQELS
KKKKKGKLPKEARQ--------------------------------KLLTWWELHYKWPY
PSESEKVALAESTGLDQKQI--NNWFINQRKRHWKPSED---------------------
------------------------------------------------------------
----------------------------------------MQFMVMDGLQ----------
-------HPHHAALYMDGH-----------------------------------------
--------------------------YMGDGPYRLG------P-----------
>gi|42560248|ref|NP_002692.2| POU domain, class 5, transcription factor 1
>isoform 1 [Homo sapiens]
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----------------------------------------------------------MA
GHLASDFAF---------------------------------------------------
------------------------------------------------------------
---------------------SPPPGG----------------------------GGDGP
GGPEPGWVDPRTWLSFQG------------------------------------------
--------------PPGGPGIGPGVGPGSEVWGIP-PCPPPYEFCG--GMAYCGPQVGVG
LVPQGGLETSQPEGEAGVGVESNSDGASPEPCTVTPGAV------------KLEKEKLEQ
NPEESQDI----KALQKELEQFAKLLKQKRITLGYTQA--------DVGLTLGVLFGKVF
SQTTICRFEALQ--LSFKNMCK--LRPLL----QKWVEEADNNENLQEICKAETLVQARK
RKRTSIEN----RVRGNLENLFLQCPKP----------------TLQQISHIAQ-----Q
LG-------------LEKD-----VVRVWFCNRRQKGKRSSSDYAQRED-----------
----------------------------------------------------FEAAGSPF
SGGPVSFPLAPGPHFGTPGY--GS------------------------------------
------------------------------------------------------------
----------------------------------------PHFTAL--------------
---------YSSVPFPEGE-----------------------------------------
----------------------------AFPPVSVT------TLGSPMHSN---
>gi|116235491|ref|NP_976034.3| POU domain, class 5, transcription factor 1
>isoform 2 [Homo sapiens]
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-------------------------MH---------------------------------
------------------------------------------------------------
--------------FYRLFLGATRRFLNPEWKGEI-DNWCVYVLTS--LLPF--------
---------------------------------------------------KIQSQDIK-
-------------ALQKELEQFAKLLKQKRITLGYTQA--------DVGLTLGVLFGKVF
SQTTICRFEALQ--LSFKNMCK--LRPLL----QKWVEEADNNENLQEICKAETLVQARK
RKRTSIEN----RVRGNLENLFLQCPKP----------------TLQQISHIAQ-----Q
LG-------------LEKD-----VVRVWFCNRRQKGKRSSSDYAQRED-----------
----------------------------------------------------FEAAGSPF
SGGPVSFPLAPGPHFGTPGY--GS------------------------------------
------------------------------------------------------------
----------------------------------------PHFTAL--------------
---------YSSVPFPEGE-----------------------------------------
----------------------------AFPPVSVT------TLGSPMHSN---
>gi|110625918|ref|NP_082292.1| Nanog homeobox [Mus musculus]
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------MSVGLPGPHSL--------------------------------
------------------------------------------------------------
--------------PSSEEASNSGNASSMPAVFHP-ENYSCLQGSA--TEMLCTEAASP-
---------------------------------------------------RPSSEDLPL
QGSPDSSTSPKQKLSSPEADKGPEEEENKVL-------------------ARKQKMRTVF
SQAQLCALKDRFQKQKYLSLQQ--MQELSSILNLSYKQVKTWFQNQRMKCKRWQKNQWLK
TSNGLIQ-----KGSAPVEYPSIHC-------------------SYPQGYLVNASGSLSM
WG-------------SQTWTNPTWSSQTWTNPTWNNQTWTNPTWSSQAWTA---------
----------------------------------------------------QSWNGQPW
NAAPLHNF--------------GEDFLQ--------------------------------
------------------------------------------------------------
----------------------------------------PYVQLQQNFS-----ASDLE
VNLEATRESHAHFSTPQAL-----------------------------------------
---------------------------ELFLNYSVT------PPGEI-------
>gi|1170314|sp|P43241.1|CDX2_MOUSE RecName: Full=Homeobox protein CDX-2;
>AltName: Full=Caudal-type homeobox protein 2
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----------------------------------------------------------MY
VSYLLDKDVSM-------------------------------------------------
------------------------------------------------------------
---------------------YPSSVR---------------------------------
------------------------------------------------------------
--------------HSGGLNLAPQNFVSPPQYPDY-GGYHVAAAAA--ATANLDSAQSPG
PSWPTAYGAPLREDWNGYAPGG-AAAA------------------------NAVAHGLNG
GSPAAAM-----GYSSPAEYHAHHHPHHHPHHPAASPS--------CASGLLQTLNLGPP
GPAATAAAEQLSPSGQRRNLCEWMRKPAQQSLGSQVKTRTKDKYRVVYTDHQRLELEKEF
HFSRYI--------------------------------------TIRRKSELAA-----T
LG-------------LSER-----QVKIWFQNRRAKERKIKKKQ-QQQQ-----------
------------------------------------------------------QQQQQQ
PPQPPPQPSQPQPG----------------------------------------------
------------------------------------------------------------
----------------------------------------ALRSV---------------
------PEPLSPVTSLQGS-----------------------------------------
--------------------------VPGSVPGVLG------PAGGVLNSTVTQ
>gi|20141282|sp|Q99626.2|CDX2_HUMAN RecName: Full=Homeobox protein CDX-2;
>AltName: Full=Caudal-type homeobox protein 2; AltName: Full=CDX-3
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----------------------------------------------------------MY
VSYLLDKDVSM-------------------------------------------------
------------------------------------------------------------
---------------------YPSSVR---------------------------------
------------------------------------------------------------
--------------HSGGLNLAPQNFVSPPQYPDY-GGYHVAAAAA--AAANLDSAQSPG
PSWPAAYGAPLREDWNGYAPGGAAAAA------------------------NAVAHGLNG
GSPAAAM-----GYSSPADYHPHHHPHHHPHHPAAAPS--------CASGLLQTLNPGPP
GPAATAAAEQLSPGGQRRNLCEWMRKPAQQSLGSQVKTRTKDKYRVVYTDHQRLELEKEF
HYSRYI--------------------------------------TIRRKAELAA-----T
LG-------------LSER-----QVKIWFQNRRAKERKINKKKLQQQQ-----------
------------------------------------------------------QQQPPQ
PPPPPPQPPQPQPG----------------------------------------------
------------------------------------------------------------
----------------------------------------PLRSV---------------
------PEPLSPVSSLQAS-----------------------------------------
--------------------------VSGSVPGVLG------PTGGVLNPTVTQ
>gi|62718869|emb|CAG25892.1| Pumilio homolog [Dugesia japonica]
------------------------------------------------------------
--------------------------MSDFHENTTERNPSGINPNVATCQIANSSIYNPL
GQVSTVISNVPNGPYYSSSFVYSDDWSMPGLSLSNTTEQLTRQISQLSYDDHSAYWP---
------------------------------------------------------------
-----------------------------------------------------PHLSMPL
SGDNRTWDTSENSISQPIPMHPGRRDTLGNESGSFMSPISKEMVALGMQVVNKVLSSSPG
TGVMCRSDIMENFYNNPSSNFGYSNGNAQPFPQSPPHYYLPSSQLYQPSTLCGTPENSQV
FGCNNQQNQSISQQPQQQSSANQQFFDPAIIAASFSNAGQGYPPQQQAPQGL--------
---------------------PPPPGLAPSHSDYMTG------------------EPTSP
LHNKQPDEEQNQYIWSPGTNNGMVHDFMGGNPGPTYGYHQQAPLYDRPTSALPTQQLYAS
QNGTL---------HHGTQTSQIQNQSAAAALFAR-SLYLAALGSG--HVP-----PATQ
QMAPQQQPPSLVPDALHTLTSMLAHGSNSYGQQPQQQPNFPSSQNNLIGQNQAALSALSA
AMSGYFLSPQIGTHAPPPTQQFSVMPGSNPTMLGAPQP-----SHTLMPATGSQLISHQG
NKPMQSGYKGVV--GNLKDGVT--RSRLL----EDFRANRLTTLTLQDISGHVVEFAQDQ
HGSRFIQQ----KLQESSHNEKTMVFREILPQCYSLMTDVFGNYVIQRFFDLGTPEQIQI
LG-------------DRIR-NQVLQLSLQMYGCRVIQKALETVSKVTQINIVRELEGSVI
KCVKDQNGNHVVQKC-VECVPPEHLDFIIDAFKDNVYSLSTHSYGCRVIQRILEHCTPEQ
TAPILAELHHFTEELVKDQY--GNYVIQHVLEHGKTEDKSKIVNLLRGRIVELSIHKFAS
NVVEKAVAHATRQERQALINEVLQDSIPVSASNAIMRTADVSGVVYGSETDGSDTDGGGS
VQRESVLYWMMKDQFANYVIQKMLDVAEQPMRKELMPKINPHLGSLRKSPSGKHIINKME
KYYMKTNQDLGILSSNSGM-----------------------------------------
------------------------------------------ACVGHM------
>gi|28573153|ref|NP_788604.1| pumilio, isoform E [Drosophila melanogaster]
------MVVLET------------------------------ASALLGGP----------
--------------------------YAQGAPA------------------LKMVQKRY-
----------IGLHHWLGPI------RSKELKEH---------IVSDDVLS---------
--------------------------------LAFNHN----------------------
------------------------------------------------------------
-----------QQLFRSQNPGLAAVATNAAAAAAAAA----AATSAASAAAAVGAPPVPN
GSLQQSQQQQQQQQQQQQQQQMHMAAASQQFLAAQQQAQNAAYAAQQATSYVINPGQEAA
PYMGMIAAAQMPYYGVAPWGMYPGNLIPQQGT----QPRRPLTPSQQGAENQPYQVIPAF
LDHTGSLLMGGPRTGTPMRLVSPAPVLVPPGATRAGP--------------PPPQGPQLY
-QPQPQTAQQNLYSQQNGSSVGGLALNTSSLTGRRDSFDRSTSAFSPSTMDYTSSGVAAA
ANAV----------NSTVAQAAAAAAAAAAARGKW-PGAMSGAASG--AYGALGAGNASA
SPLGAPITPP--PSAQSCLLGSRAPGAESRQ-RQQQQQQLAA-VGLPA---TAAAAQAAV
AAAANNMF----GSNSSIFSNPLAIPGTAAVAAAAAAA--------AAANSRQVAATAAA
AAAVAAAAGGVG--GAPQPG----RSRLL----EDFRNQRYPNLQLRDLANHIVEFSQDQ
HGSRFIQQ----KLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNT
LG-------------MQVKG-HVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVL
KCVKDQNGNHVVQKC-IECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQ
TTPILDELHEHTEQLIQDQY--GNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFAS
NVVEKCVTHATRGERTGLIDEV-------------------------------------C
TFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAALRKYTYGKHINAKLE
KYYMKITNPITVGTGAGGVPAASSAAAVSSGATSASVTACTSGSSTTTTSTTNSLASPTI
CSVQENGSAMVVEPSSPDASESSSSVVSGAVNSSLG------PIGPPTNGNVVL
>gi|45551850|ref|NP_731316.2| pumilio, isoform B [Drosophila melanogaster]
MMKLLHDFILDARTAEDVALTQEMITTSTAKKLWEKSDGKGVSSSTPGGPLHPLQIPGIG
DPSSVWKDHTWSTQGENILVPPPSRAYAHGGASDTSNSGNAGILSPRDSTCAKVVEYVFS
GSPTNKDSSLSGLEPHLRNLKFDDNDKSRDDKEKANSPFDTNGLKKDDQVTNSNGVVNGI
DDDKGFNRTPGSRQPSPAEESQPRPPNLLFPPLPFNHMLMDHGQGMGGGLGGVVGSGNGV
GGGSGGGGAGGAYAAHQQMAAQMSQLQPPMMNGVGGGMPMAAQSPMLNHQAAGPNHMESP
GNLLQQQNFDVQQLFRSQNPGLAAVATNAAAAAAAAA----AATSAASAAAAVGAPPVPN
GSLQQSQQQQQQQQQQQQQQQMHMAAASQQFLAAQQQAQNAAYAAQQATSYVINPGQEAA
PYMGMIAAAQMPYYGVAPWGMYPGNLIPQQGT----QPRRPLTPSQQGAENQPYQVIPAF
LDHTGSLLMGGPRTGTPMRLVSPAPVLVPPGATRAGP--------------PPPQGPQLY
-QPQPQTAQQNLYSQQNGSSVGGLALNTSSLTGRRDSFDRSTSAFSPSTMDYTSSGVAAA
ANAV----------NSTVAQAAAAAAAAAAARGKW-PGAMSGAASG--AYGALGAGNASA
SPLGAPITPP--PSAQSCLLGSRAPGAESRQ-RQQQQQQLAA-VGLPA---TAAAAQAAV
AAAANNMF----GSNSSIFSNPLAIPGTAAVAAAAAAA--------AAANSRQVAATAAA
AAAVAAAAGGVG--GAPQPG----RSRLL----EDFRNQRYPNLQLRDLANHIVEFSQDQ
HGSRFIQQ----KLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNT
LG-------------MQVKG-HVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVL
KCVKDQNGNHVVQKC-IECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQ
TTPILDELHEHTEQLIQDQY--GNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFAS
NVVEKCVTHATRGERTGLIDEV-------------------------------------C
TFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAALRKYTYGKHINAKLE
KYYMKITNPITVGTGAGGVPAASSAAAVSSGATSASVTACTSGSSTTTTSTTNSLASPTI
CSVQENGSAMVVEPSSPDASESSSSVVSGAVNSSLG------PIGPPTNGNVVL
_______________________________________________
EMBOSS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/emboss
