uploading an allignment in FASTA format
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marina.g.g...@gmail.com
May 5, 2015, 12:23:25 PM5/5/15
to evcou...@googlegroups.com
Hello,
I have an allignment file that I want to use to calculate EVcouplings scores.When I run EVcouplings i get an error: "progress stopped in : making/finding family alignment".
What could be the problem.
Best
The allignment file looks like this, and it contains concatenated sequences of 2 proteins that presumably interact:
>0202|sp|P28223-P29992
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
-----------------------------------------------------mdilceentslssttnslm
qlnddtrlysndfnsgeantsdafnwtvdsenrtnlscegclspsclsllhlqeknwsalltavviiltiaG
NILVIMAVSLE-KKLQ-----NATNYFLMSLAIADMLLGFLVMPVSMLTILY-------gYRW---PLPS--
---KLCAVWIYLDVLFSTASIMHLCAI----SLDRYVAI---Q-NP----IHH-SRFNS-----RTK-----
----------A--F-----LKI----IAVWTISVG-ISMPI----PVFGLQDDSKVFK--------------
-------------------------------EGSCLLADDNF------------------------VLIGSF
--VSF--FI-PLTIMVITYF-LTIKSLQKEATLCVSDLGtraklasfsflpqssls----------------
------------------------------------------------------------------------
------------------------------------------------------------------------
-----------seklfqrsihrepgsytgRRTMQSISNEQKACKVLGIVFFLFVVMWCP-----FFIT----
-NIMAVICKES----------CNe-dVIGALLN-VF-VWIGYLSSAVNPLVYtlfnktyrsafsryiqcqyk
enkkplqlilvntipalaykssqlqmgqkknskqdakttdndcsmvalgkqhseeaskdnsdgvnekvscv-
------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------MTLESM------------------------------------
--MACCLSDEVKESKRINAEIEKQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGYSEEDKRGFT
K---------------LVYQNIFTAMQAMIRAMETLKIL--YKYEQNKANALLIREV--DV--EKVT----T
FEHQYVSAIKTLWEDPGIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPTTGIIEYPFD
LENIIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNS
SVILFLNKKDLLEDKIL--YSHLVDYFPEFDGPQRDA------------QAAREFILKMFVDLNP-------
-----DSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV
>0001|sp|P41595-P29992
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
-malsyrvselqstipehilqstfvhvissnwsglqtesipeemkqiveeqgnklhwaallilmviiptigG
NTLVILAVSLE-KKLQ-----YATNYFLMSLAVADLLVGLFVMPIALLTIMF-------eAMW---PLPL--
---VLCPAWLFLDVLFSTASIMHLCAI----SVDRYIAI---K-KP----IQA-NQYNS-----RAT-----
----------A--F-----IKI----TVVWLISIG-IAIPV----PIKGIETDVDNPN--------------
-------------------------------NITCVLTKERFG---------------------DFMLFGSL
--AAF--FT-PLAIMIVTYF-LTIHALQKKAYLVKNKPPqrltwltvstvfqrdetpcsspekva-------
------------------------------------------------------------------------
------------------------------------------------------------------------
--mldgsrkdkalpnsgdetlmrrtstigKKSVQTISNEQRASKVLGIVFFLFLLMWCP-----FFIT----
-NITLVLCDSC----------NQ--tTLQMLLE-IF-VWIGYVSSGVNPLVYtlfnktfrdafgryitcnyr
atksvktlrkrsskiyfrnpmaenskffkkhgirnginpamyqspmrlrsstiqsssiilldtllltenegd
kteeqvsyv---------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------MTLESM------------------------------------
--MACCLSDEVKESKRINAEIEKQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGYSEEDKRGFT
K---------------LVYQNIFTAMQAMIRAMETLKIL--YKYEQNKANALLIREV--DV--EKVT----T
FEHQYVSAIKTLWEDPGIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPTTGIIEYPFD
LENIIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNS
SVILFLNKKDLLEDKIL--YSHLVDYFPEFDGPQRDA------------QAAREFILKMFVDLNP-------
-----DSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV
>0123|sp|P28335-P29992
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
--mvnlrnavhsflvhligllvwqcdisvspvaaivtdifntsdggrfkfpdgvqnwpalsiviiiimtigG
NILVIMAVSME-KKLH-----NATNYFLMSLAIADMLVGLLVMPLSLLAILY-------dYVW---PLPR--
---YLCPVWISLDVLFSTASIMHLCAI----SLDRYVAI---R-NP----IEH-SRFNS-----RTK-----
----------A--I-----MKI----AIVWAISIG-VSVPI----PVIGLRDEEKVFV--------------
------------------------------nNTTCVLNDPNF------------------------VLIGSF
--VAF--FI-PLTIMVITYC-LTIYVLRRQALMLLHGHTeeppglsldflkcckrntaee------------
------------------------------------------------------------------------
------------------------------------------------------------------------
-------ensanpnqdqnarrrkkkerrpRGTMQAINNERKASKVLGIVFFVFLIMWCP-----FFIT----
-NILSVLCEKS----------CNq-kLMEKLLN-VF-VWIGYVCSGINPLVYtlfnkiyrrafsnylrcnyk
vekkppvrqiprvaatalsgrelnvniyrhtnepviekasdnepgiemqvenlelpvnpssvvserissv--
------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------MTLESM------------------------------------
--MACCLSDEVKESKRINAEIEKQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGYSEEDKRGFT
K---------------LVYQNIFTAMQAMIRAMETLKIL--YKYEQNKANALLIREV--DV--EKVT----T
FEHQYVSAIKTLWEDPGIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPTTGIIEYPFD
LENIIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNS
SVILFLNKKDLLEDKIL--YSHLVDYFPEFDGPQRDA------------QAAREFILKMFVDLNP-------
-----DSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV
I have an allignment file that I want to use to calculate EVcouplings scores.When I run EVcouplings i get an error: "progress stopped in : making/finding family alignment".
What could be the problem.
Best
The allignment file looks like this, and it contains concatenated sequences of 2 proteins that presumably interact:
>0202|sp|P28223-P29992
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
-----------------------------------------------------mdilceentslssttnslm
qlnddtrlysndfnsgeantsdafnwtvdsenrtnlscegclspsclsllhlqeknwsalltavviiltiaG
NILVIMAVSLE-KKLQ-----NATNYFLMSLAIADMLLGFLVMPVSMLTILY-------gYRW---PLPS--
---KLCAVWIYLDVLFSTASIMHLCAI----SLDRYVAI---Q-NP----IHH-SRFNS-----RTK-----
----------A--F-----LKI----IAVWTISVG-ISMPI----PVFGLQDDSKVFK--------------
-------------------------------EGSCLLADDNF------------------------VLIGSF
--VSF--FI-PLTIMVITYF-LTIKSLQKEATLCVSDLGtraklasfsflpqssls----------------
------------------------------------------------------------------------
------------------------------------------------------------------------
-----------seklfqrsihrepgsytgRRTMQSISNEQKACKVLGIVFFLFVVMWCP-----FFIT----
-NIMAVICKES----------CNe-dVIGALLN-VF-VWIGYLSSAVNPLVYtlfnktyrsafsryiqcqyk
enkkplqlilvntipalaykssqlqmgqkknskqdakttdndcsmvalgkqhseeaskdnsdgvnekvscv-
------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------MTLESM------------------------------------
--MACCLSDEVKESKRINAEIEKQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGYSEEDKRGFT
K---------------LVYQNIFTAMQAMIRAMETLKIL--YKYEQNKANALLIREV--DV--EKVT----T
FEHQYVSAIKTLWEDPGIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPTTGIIEYPFD
LENIIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNS
SVILFLNKKDLLEDKIL--YSHLVDYFPEFDGPQRDA------------QAAREFILKMFVDLNP-------
-----DSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV
>0001|sp|P41595-P29992
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
-malsyrvselqstipehilqstfvhvissnwsglqtesipeemkqiveeqgnklhwaallilmviiptigG
NTLVILAVSLE-KKLQ-----YATNYFLMSLAVADLLVGLFVMPIALLTIMF-------eAMW---PLPL--
---VLCPAWLFLDVLFSTASIMHLCAI----SVDRYIAI---K-KP----IQA-NQYNS-----RAT-----
----------A--F-----IKI----TVVWLISIG-IAIPV----PIKGIETDVDNPN--------------
-------------------------------NITCVLTKERFG---------------------DFMLFGSL
--AAF--FT-PLAIMIVTYF-LTIHALQKKAYLVKNKPPqrltwltvstvfqrdetpcsspekva-------
------------------------------------------------------------------------
------------------------------------------------------------------------
--mldgsrkdkalpnsgdetlmrrtstigKKSVQTISNEQRASKVLGIVFFLFLLMWCP-----FFIT----
-NITLVLCDSC----------NQ--tTLQMLLE-IF-VWIGYVSSGVNPLVYtlfnktfrdafgryitcnyr
atksvktlrkrsskiyfrnpmaenskffkkhgirnginpamyqspmrlrsstiqsssiilldtllltenegd
kteeqvsyv---------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------MTLESM------------------------------------
--MACCLSDEVKESKRINAEIEKQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGYSEEDKRGFT
K---------------LVYQNIFTAMQAMIRAMETLKIL--YKYEQNKANALLIREV--DV--EKVT----T
FEHQYVSAIKTLWEDPGIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPTTGIIEYPFD
LENIIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNS
SVILFLNKKDLLEDKIL--YSHLVDYFPEFDGPQRDA------------QAAREFILKMFVDLNP-------
-----DSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV
>0123|sp|P28335-P29992
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
--mvnlrnavhsflvhligllvwqcdisvspvaaivtdifntsdggrfkfpdgvqnwpalsiviiiimtigG
NILVIMAVSME-KKLH-----NATNYFLMSLAIADMLVGLLVMPLSLLAILY-------dYVW---PLPR--
---YLCPVWISLDVLFSTASIMHLCAI----SLDRYVAI---R-NP----IEH-SRFNS-----RTK-----
----------A--I-----MKI----AIVWAISIG-VSVPI----PVIGLRDEEKVFV--------------
------------------------------nNTTCVLNDPNF------------------------VLIGSF
--VAF--FI-PLTIMVITYC-LTIYVLRRQALMLLHGHTeeppglsldflkcckrntaee------------
------------------------------------------------------------------------
------------------------------------------------------------------------
-------ensanpnqdqnarrrkkkerrpRGTMQAINNERKASKVLGIVFFVFLIMWCP-----FFIT----
-NILSVLCEKS----------CNq-kLMEKLLN-VF-VWIGYVCSGINPLVYtlfnkiyrrafsnylrcnyk
vekkppvrqiprvaatalsgrelnvniyrhtnepviekasdnepgiemqvenlelpvnpssvvserissv--
------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------MTLESM------------------------------------
--MACCLSDEVKESKRINAEIEKQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGYSEEDKRGFT
K---------------LVYQNIFTAMQAMIRAMETLKIL--YKYEQNKANALLIREV--DV--EKVT----T
FEHQYVSAIKTLWEDPGIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPTTGIIEYPFD
LENIIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNS
SVILFLNKKDLLEDKIL--YSHLVDYFPEFDGPQRDA------------QAAREFILKMFVDLNP-------
-----DSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV
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