From 2df9339bdc230e2db3c36ed85960bcd13a225188 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Fri, 2 Aug 2013 17:17:57 +0100 Subject: [PATCH] add results of one Jpred test --- binaries/src/jpred/tests/res_d16vpa_.align | 78 ++++++ binaries/src/jpred/tests/res_d16vpa_.concise | 25 ++ binaries/src/jpred/tests/res_d16vpa_.hmm | 356 +++++++++++++++++++++++++ binaries/src/jpred/tests/res_d16vpa_.jnet | 12 + binaries/src/jpred/tests/res_d16vpa_.profile | 365 ++++++++++++++++++++++++++ binaries/src/jpred/tests/res_d16vpa_.pssm | 356 +++++++++++++++++++++++++ binaries/src/jpred/tests/res_d16vpa_.res | 114 ++++++++ binaries/src/jpred/tests/todo.bash | 8 +- 8 files changed, 1310 insertions(+), 4 deletions(-) create mode 100644 binaries/src/jpred/tests/res_d16vpa_.align create mode 100644 binaries/src/jpred/tests/res_d16vpa_.concise create mode 100644 binaries/src/jpred/tests/res_d16vpa_.hmm create mode 100644 binaries/src/jpred/tests/res_d16vpa_.jnet create mode 100644 binaries/src/jpred/tests/res_d16vpa_.profile create mode 100644 binaries/src/jpred/tests/res_d16vpa_.pssm create mode 100644 binaries/src/jpred/tests/res_d16vpa_.res diff --git a/binaries/src/jpred/tests/res_d16vpa_.align b/binaries/src/jpred/tests/res_d16vpa_.align new file mode 100644 index 0000000..e846252 --- /dev/null +++ b/binaries/src/jpred/tests/res_d16vpa_.align @@ -0,0 +1,78 @@ +>QUERY +SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA +YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL +HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES +WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG +YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL +>UniRef90_Q00028 +-----PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD +SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ +LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ +RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG +FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA-------------- +>UniRef90_Q8B635 +-----PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN +SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS +IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH +RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG +FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA-------------- +>UniRef90_Q9E205 +-----PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS +ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS +SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE +NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG +FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS-------------- +>UniRef90_Q88530 +--LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE +NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L +NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ +GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG +YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS-------------- +>UniRef90_B4XS08 +------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S +EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG +VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ +YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG +FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP------------- +>UniRef90_P09265 +---PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S +TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT +TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE +RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG +FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE----------- +>UniRef90_Q2QBC8 +------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA +HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL +HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ +ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG +YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL------------------- +>UniRef90_Q90603 +---------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK +NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD +LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ +ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV +YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD---------------- +>UniRef90_O89246 +--------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE +EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP +SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ +LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA +YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR---- +>UniRef90_Q5PP87 +----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA +PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD +-------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ +ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG +YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG---------------------------- +>UniRef90_Q65819 +----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL +AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T +AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ +RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG +FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS--------------- +>UniRef90_O56869 +-RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS +GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV +GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES +-QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA +YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP------------- diff --git a/binaries/src/jpred/tests/res_d16vpa_.concise b/binaries/src/jpred/tests/res_d16vpa_.concise new file mode 100644 index 0000000..38a9914 --- /dev/null +++ b/binaries/src/jpred/tests/res_d16vpa_.concise @@ -0,0 +1,25 @@ +align1;QUERY:S,R,M,P,S,P,P,M,P,V,P,P,A,A,L,F,N,R,L,L,D,D,L,G,F,S,A,G,P,A,L,C,T,M,L,D,T,W,N,E,D,L,F,S,A,L,P,T,N,A,D,L,Y,R,E,C,K,F,L,S,T,L,P,S,D,V,V,E,W,G,D,A,Y,V,P,E,R,T,Q,I,D,I,R,A,H,G,D,V,A,F,P,T,L,P,A,T,R,D,G,L,G,L,Y,Y,E,A,L,S,R,F,F,H,A,E,L,R,A,R,E,E,S,Y,R,T,V,L,A,N,F,C,S,A,L,Y,R,Y,L,R,A,S,V,R,Q,L,H,R,Q,A,H,M,R,G,R,D,R,D,L,G,E,M,L,R,A,T,I,A,D,R,Y,Y,R,E,T,A,R,L,A,R,V,L,F,L,H,L,Y,L,F,L,T,R,E,I,L,W,A,A,Y,A,E,Q,M,M,R,P,D,L,F,D,C,L,C,C,D,L,E,S,W,R,Q,L,A,G,L,F,Q,P,F,M,F,V,N,G,A,L,T,V,R,G,V,P,I,E,A,R,R,L,R,E,L,N,H,I,R,E,H,L,N,L,P,L,V,R,S,A,A,T,E,E,P,G,A,P,L,T,T,P,P,T,L,H,G,N,Q,A,R,A,S,G,Y,F,M,V,L,I,R,A,K,L,D,S,Y,S,S,F,T,T,S,P,S,E,A,V,M,R,E,H,A,Y,S,R,A,P,T,K,N,N,Y,G,S,T,I,E,G,L,L,D,L,P,D,D,D,A,P,E,E,A,G,L,A,A,P,R,L,S,F,L, +align2;UniRef90_Q00028:-,-,-,-,-,P,P,K,A,T,S,P,T,A,L,Y,Q,R,L,Q,A,E,L,G,F,P,E,G,Q,A,M,L,F,A,M,E,K,W,N,E,D,M,F,S,A,I,P,V,H,V,D,L,Y,T,E,I,A,L,L,S,T,S,V,N,E,V,V,K,A,G,L,D,S,L,P,I,P,T,E,V,D,L,N,A,H,G,S,E,P,F,P,E,V,P,A,L,E,D,E,L,E,T,Y,V,I,S,A,Q,R,F,Y,L,S,E,L,R,A,R,E,E,H,Y,S,R,L,L,R,G,Y,C,V,A,L,L,H,Y,L,Y,G,S,A,K,R,Q,L,R,G,A,-,-,-,G,S,D,S,A,L,M,H,K,F,K,Q,V,V,R,D,R,Y,Y,R,E,T,A,N,L,A,R,L,L,Y,L,H,L,Y,I,S,V,T,R,E,V,S,W,R,L,H,A,S,Q,V,V,N,Q,G,I,F,V,S,L,H,Y,T,W,P,Q,R,R,K,F,E,C,L,F,H,P,V,L,F,N,H,G,V,V,I,L,E,N,D,P,L,E,F,N,D,L,Q,R,I,N,Y,R,R,R,E,L,G,L,P,L,I,R,A,G,L,I,E,E,E,N,L,P,L,E,S,E,P,T,F,S,G,K,L,P,R,T,I,G,F,L,T,H,Q,I,R,T,K,M,E,A,Y,S,N,A,H,P,S,T,P,L,F,P,L,A,E,H,S,Y,S,R,I,D,G,R,L,S,Y,G,T,T,A,E,A,M,M,D,P,P,S,P,S,A,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +align3;UniRef90_Q8B635:-,-,-,-,-,P,I,K,A,S,S,P,S,S,L,I,K,N,L,L,D,E,L,N,F,P,E,G,P,S,L,L,S,S,M,E,K,W,N,E,D,L,F,S,C,I,P,R,F,L,E,I,Y,I,E,N,S,I,L,S,T,S,V,D,E,V,I,K,N,L,D,N,S,L,N,Y,D,D,V,I,D,F,Q,V,H,G,P,E,T,F,P,K,T,P,L,L,E,E,E,L,E,N,Y,V,T,S,V,Q,K,Y,F,L,S,E,L,K,A,R,E,V,T,Y,S,F,L,L,T,K,Y,C,K,A,L,L,L,Y,L,R,Y,N,T,K,S,S,I,K,G,-,-,-,-,-,-,N,K,D,I,N,Q,K,F,K,Q,N,V,R,E,R,Y,Y,R,E,V,A,N,I,A,R,L,L,Y,L,H,L,Y,L,S,V,T,R,E,V,S,W,K,L,H,A,D,Q,V,L,L,Q,S,V,F,V,S,L,S,Y,S,W,S,H,R,R,Q,F,E,C,I,F,H,P,I,L,F,N,H,G,I,V,N,L,E,N,N,P,L,T,F,K,E,L,Q,K,I,N,Y,R,R,H,I,L,G,L,P,L,I,R,A,G,L,V,E,E,D,N,Q,P,L,M,I,P,P,E,F,S,S,K,L,P,R,T,I,G,F,L,T,Q,Q,I,R,A,K,M,E,A,Y,S,D,N,H,P,V,T,P,K,F,P,R,I,E,H,S,Y,A,K,P,I,D,P,I,N,Y,G,T,T,I,E,A,M,M,D,P,P,S,P,S,A,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +align4;UniRef90_Q9E205:-,-,-,-,-,P,P,R,V,A,S,P,A,V,L,Y,Q,Q,L,I,N,D,L,H,F,S,E,G,P,R,I,I,A,L,L,E,T,C,N,E,D,I,F,S,C,F,P,L,N,E,D,L,Y,T,D,T,I,V,F,S,T,N,P,S,D,I,I,E,L,E,T,S,E,T,P,E,-,-,P,I,N,L,I,T,K,G,-,C,D,L,P,S,L,P,S,T,Y,T,E,L,P,M,Y,V,E,N,V,Q,N,T,F,F,T,E,L,R,V,R,E,K,A,Y,L,R,L,L,I,L,Y,C,K,S,L,L,R,H,L,Q,G,I,S,R,R,S,S,V,G,A,R,S,Q,D,C,E,H,K,Y,I,T,Q,F,K,Q,S,I,R,L,R,Y,Y,R,E,V,A,K,L,A,R,L,L,Y,L,H,L,Y,I,T,V,T,R,Q,F,S,W,R,L,F,A,Q,Q,S,K,Y,P,D,V,F,A,A,M,K,F,M,W,L,E,N,R,Q,F,T,C,A,F,H,P,I,L,C,N,H,G,I,V,L,L,E,G,K,P,L,S,S,Q,R,L,R,E,V,N,Y,R,R,R,Q,L,G,L,P,L,V,R,C,A,L,I,E,E,K,G,V,P,L,V,Q,R,P,E,F,S,A,H,M,P,R,S,L,G,F,L,T,H,H,I,K,A,K,L,D,V,Y,S,S,K,H,S,Q,E,P,G,N,V,R,V,D,H,P,Y,A,R,N,V,N,N,I,N,Y,G,S,S,V,E,A,M,I,V,S,P,P,S,P,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +align5;UniRef90_Q88530:-,-,L,P,S,P,E,-,A,A,S,P,N,L,L,Y,D,R,L,I,L,E,L,D,F,A,E,G,P,S,L,L,A,K,L,E,R,V,N,V,D,L,F,S,C,L,P,L,N,S,H,L,Y,K,H,A,K,I,L,S,T,C,P,R,E,V,L,D,A,V,Y,E,N,T,W,Q,Y,T,A,L,N,L,N,E,H,G,K,S,S,I,P,P,V,P,A,S,K,D,D,L,P,A,Y,V,T,A,V,Q,E,F,Y,L,E,E,L,E,A,R,E,Q,I,Y,A,K,L,F,F,G,Y,C,R,A,L,I,M,H,I,I,K,S,V,-,-,L,N,E,S,R,G,V,R,V,S,D,D,Y,V,Q,N,K,A,R,W,Y,I,S,N,N,Y,Y,R,D,A,V,R,I,A,K,L,L,Y,L,H,L,Y,L,S,T,T,E,I,V,S,Q,R,L,E,A,M,Q,T,S,L,Q,D,L,F,V,Y,L,R,C,E,W,G,Q,G,R,Q,F,W,C,I,F,Q,P,M,I,Y,N,H,G,V,P,M,I,E,G,R,A,L,T,S,L,E,L,G,S,S,N,Y,I,R,S,E,L,G,L,P,L,I,R,C,E,L,L,E,E,L,E,S,P,V,V,F,P,P,T,F,T,A,T,A,P,R,S,S,G,Y,L,F,H,N,I,R,A,K,M,E,L,Y,S,N,I,H,P,S,P,Q,L,S,G,L,S,D,H,T,Y,V,R,T,H,V,P,V,N,Y,G,T,T,V,E,V,L,L,D,A,S,D,P,D,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +align6;UniRef90_B4XS08:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,F,P,E,A,S,T,I,L,S,T,F,E,L,M,N,M,D,L,F,S,C,L,P,R,N,E,D,L,Y,R,N,A,A,L,L,S,G,S,V,T,E,V,I,E,A,-,-,S,E,I,P,I,D,G,E,I,D,L,N,A,H,G,S,K,Q,L,P,I,P,P,S,N,E,W,E,I,P,N,Y,V,E,A,V,Q,Q,F,F,L,S,E,L,R,A,R,E,E,S,Y,L,K,L,F,L,G,Y,C,R,A,I,V,N,Y,I,K,S,A,A,T,R,G,V,R,G,C,R,I,M,D,R,K,S,E,A,N,K,R,M,R,R,M,I,A,D,R,Y,Y,R,E,A,A,R,L,A,K,V,L,Y,L,H,L,Y,L,S,V,A,R,E,I,S,S,R,L,C,A,T,Q,M,Q,V,Q,N,V,F,V,Y,M,R,Y,E,W,Q,Q,Y,R,Q,F,T,C,L,F,H,P,I,M,F,N,H,G,V,V,L,L,N,G,E,P,L,Q,A,Q,K,L,R,E,V,N,Y,I,R,F,K,L,G,L,P,V,I,R,C,G,L,V,E,E,H,D,K,P,L,V,E,E,P,R,F,Y,G,N,L,P,R,S,S,G,F,L,T,E,L,I,R,S,K,M,E,A,Y,S,E,L,R,P,T,S,P,S,S,I,S,N,D,H,T,Y,A,K,Q,L,D,K,V,N,F,G,S,T,R,E,A,I,L,D,T,I,D,T,E,G,P,-,-,-,-,-,-,-,-,-,-,-,-,-, +align7;UniRef90_P09265:-,-,-,P,S,P,P,W,V,A,S,P,K,I,L,Y,Q,Q,L,I,R,D,L,D,F,S,E,G,P,R,L,L,S,C,L,E,T,W,N,E,D,L,F,S,C,F,P,I,N,E,D,L,Y,S,D,M,M,V,L,S,P,D,P,D,D,V,I,-,-,-,-,S,T,V,S,T,K,D,H,V,N,L,T,T,R,G,S,V,R,L,P,S,P,P,K,Q,P,T,G,L,P,A,Y,V,Q,E,V,Q,D,S,F,T,V,E,L,R,A,R,E,E,A,Y,T,K,L,L,V,T,Y,C,K,S,I,I,R,Y,L,Q,G,T,A,K,R,T,T,I,G,L,N,I,Q,N,P,D,Q,K,A,Y,T,Q,L,R,Q,S,I,L,L,R,Y,Y,R,E,V,A,S,L,A,R,L,L,Y,L,H,L,Y,L,T,V,T,R,E,F,S,W,R,L,Y,A,S,Q,S,A,H,P,D,V,F,A,A,L,K,F,T,W,T,E,R,R,Q,F,T,C,A,F,H,P,V,L,C,N,H,G,I,V,L,L,E,G,K,P,L,T,A,S,A,L,R,E,I,N,Y,R,R,R,E,L,G,L,P,L,V,R,C,G,L,V,E,E,N,K,S,P,L,V,Q,Q,P,S,F,S,V,H,L,P,R,S,V,G,F,L,T,H,H,I,K,R,K,L,D,A,Y,A,V,K,H,P,Q,E,P,R,H,V,R,A,D,H,P,Y,A,K,V,V,E,N,R,N,Y,G,S,S,I,E,A,M,I,L,A,P,-,-,P,S,P,S,E,-,-,-,-,-,-,-,-,-,-,-, +align8;UniRef90_Q2QBC8:-,-,-,-,-,-,-,-,-,-,-,-,A,A,L,Y,N,R,L,L,E,D,L,G,F,G,D,G,P,A,L,C,T,I,L,D,S,W,N,E,D,L,F,S,G,L,P,A,N,P,D,L,Y,R,E,C,R,F,L,S,T,L,P,G,D,V,V,V,W,G,D,A,H,A,P,D,R,G,P,I,D,I,R,A,H,G,S,A,P,F,P,S,L,P,A,R,R,E,G,L,P,A,Y,C,E,A,L,T,R,F,F,H,S,E,L,R,A,R,E,E,S,Y,R,R,V,L,A,N,F,C,S,A,L,Y,R,Y,L,R,A,S,T,R,Q,L,H,R,Q,A,A,L,K,G,R,P,R,D,L,Q,E,M,L,R,A,A,V,A,E,R,Y,Y,R,E,T,A,R,L,A,R,V,L,F,L,H,L,Y,L,F,L,V,R,E,I,L,W,A,V,Y,A,E,Q,V,M,R,Q,D,L,F,E,G,L,R,C,D,L,E,Q,A,R,Q,L,S,C,L,F,Q,P,L,L,F,V,H,G,A,L,S,V,G,G,E,P,V,S,P,A,R,L,R,E,L,N,H,V,R,E,R,L,N,L,P,L,I,R,S,A,A,T,E,E,P,G,A,A,L,T,A,A,P,A,L,Q,T,Q,R,A,R,S,S,G,Y,F,M,T,L,I,R,V,K,L,D,A,Y,S,E,W,S,A,G,S,E,G,A,V,L,R,E,H,A,Y,S,R,R,R,E,R,T,N,Y,G,S,S,I,E,G,L,L,E,L,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +align9;UniRef90_Q90603:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,Y,T,R,L,L,H,E,L,D,F,V,E,G,P,S,I,L,A,R,L,E,K,I,N,V,D,L,F,S,C,F,P,H,N,K,H,L,Y,E,H,A,K,I,L,S,V,S,P,S,E,V,L,E,E,L,S,K,N,T,W,T,Y,T,A,L,N,L,N,E,H,G,E,V,A,L,P,M,P,P,T,T,K,A,D,L,P,S,Y,V,D,D,I,Q,N,F,Y,L,G,E,L,E,A,R,E,K,S,Y,A,T,M,F,Y,G,Y,C,R,A,L,A,E,Y,I,R,Q,S,A,I,K,D,L,R,D,A,-,-,R,V,E,D,K,N,I,G,A,C,S,K,A,R,Q,Y,I,A,E,R,Y,Y,R,E,A,F,A,N,V,L,Y,V,H,L,Y,L,S,T,T,R,D,V,S,Q,R,L,E,A,S,Q,M,G,R,Q,N,I,F,V,Y,L,K,C,E,W,L,Q,E,R,H,F,H,C,L,F,Q,P,V,I,F,N,H,G,V,V,I,V,E,G,R,V,L,T,A,P,E,L,R,A,Q,N,Y,I,R,S,E,F,G,L,P,L,I,R,C,K,L,V,E,E,P,D,M,P,L,I,S,P,P,P,F,S,G,D,A,P,R,A,S,V,Y,L,L,Q,C,I,R,S,K,L,E,V,Y,S,S,H,P,P,N,P,Q,L,H,V,H,K,E,H,V,H,Q,K,L,E,S,P,P,N,Y,G,T,T,V,E,A,L,L,M,D,S,S,D,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +align10;UniRef90_O89246:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,E,L,D,F,T,E,G,P,S,L,L,S,R,L,E,K,L,N,V,D,L,F,S,C,F,P,I,N,G,H,L,Y,E,H,A,T,L,L,S,V,S,P,S,E,V,L,D,A,A,S,E,E,K,W,A,Y,T,A,I,N,L,N,E,H,C,G,M,E,V,P,R,P,P,L,T,K,D,G,L,P,V,Y,V,T,E,I,Q,K,F,F,S,M,E,L,E,A,R,E,K,S,Y,V,T,L,L,C,G,Y,C,R,A,L,A,C,Y,L,R,Q,G,A,N,E,P,S,R,C,D,M,C,V,G,G,S,-,-,-,-,E,T,P,R,R,S,I,A,G,A,Y,Y,R,E,A,A,R,F,A,R,L,L,Y,M,H,L,Y,L,S,V,T,R,D,V,S,R,R,L,E,A,S,Q,R,K,R,Q,N,L,F,A,H,L,R,C,D,W,H,Q,L,R,H,F,Q,C,L,F,Q,P,V,I,F,N,H,G,V,V,I,V,E,G,R,A,L,T,A,A,E,L,R,T,Q,N,Y,V,R,S,E,L,G,L,P,V,M,R,C,E,L,V,E,E,R,G,M,P,L,T,A,P,P,A,F,L,A,N,A,P,R,A,S,A,Y,L,F,Q,C,I,K,S,K,L,E,V,Y,S,L,M,H,P,P,R,P,R,S,S,A,R,G,E,S,G,R,A,G,K,A,G,P,S,H,G,T,I,V,K,A,M,L,R,D,S,T,H,P,G,P,A,I,A,D,I,A,A,A,R,-,-,-,-, +align11;UniRef90_Q5PP87:-,-,-,-,-,-,-,-,-,-,S,P,D,A,L,Y,Q,R,L,I,S,D,L,A,F,D,E,G,P,A,L,L,G,A,M,E,R,W,N,E,D,L,F,S,C,L,P,G,N,E,D,L,Y,A,R,L,V,M,L,S,A,S,A,D,E,V,A,A,Q,V,R,A,P,T,A,D,A,S,-,V,D,L,G,V,P,G,A,E,P,M,P,R,V,P,A,V,E,E,E,L,P,A,Y,V,A,A,V,E,R,F,F,V,S,T,L,R,A,R,E,E,R,Y,A,R,L,L,D,A,Y,C,R,A,V,L,R,Y,L,H,A,Q,A,R,R,D,-,-,-,-,-,-,-,-,-,-,-,-,-,E,G,K,L,R,Q,L,V,R,G,R,Y,Y,R,D,V,A,R,L,A,P,W,L,F,L,H,L,Y,V,A,T,A,R,E,L,S,W,R,L,H,A,D,Q,V,V,A,Q,D,V,F,M,S,L,R,Y,E,W,D,Q,A,R,Q,L,T,C,L,F,H,P,V,L,F,N,H,G,V,V,L,L,S,G,A,P,V,P,A,A,Q,L,R,A,V,N,H,R,R,R,E,L,G,L,P,L,V,R,A,G,L,I,E,E,D,G,A,D,L,V,E,E,P,P,F,S,A,A,L,P,R,A,A,G,Y,L,S,H,Q,V,R,I,K,M,E,A,Y,S,-,-,-,-,-,-,-,-,R,E,Y,R,D,H,T,Y,C,R,P,P,S,P,V,S,Y,G,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +align12;UniRef90_Q65819:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,R,M,Q,A,E,L,G,F,P,D,G,P,A,L,L,R,A,M,E,R,W,N,E,D,L,F,S,C,L,P,T,N,A,D,L,Y,A,D,A,A,L,L,S,A,D,A,D,A,V,V,G,A,M,Y,L,A,V,P,D,A,E,R,L,D,L,N,A,H,A,N,Q,P,L,P,A,P,P,A,S,E,E,G,L,P,E,Y,V,A,G,V,Q,A,H,F,L,A,E,L,R,A,R,E,E,R,Y,A,G,L,F,L,G,Y,C,R,A,L,L,Q,H,L,R,A,-,-,-,-,T,A,A,R,G,R,G,A,A,G,A,G,A,Q,A,D,R,L,R,Q,L,V,A,A,R,Y,Y,R,E,A,S,R,L,A,R,L,A,F,A,H,M,Y,V,A,T,A,R,E,V,S,W,R,L,H,S,Q,Q,S,Q,A,Q,G,V,F,V,S,L,Y,Y,A,W,P,Q,R,R,Q,F,T,C,L,F,H,P,V,L,F,N,H,G,V,V,A,L,E,D,G,F,L,D,A,A,E,L,R,R,L,N,Y,R,R,R,E,L,G,L,P,L,V,R,A,G,L,V,E,V,E,V,G,P,L,V,E,E,P,P,F,S,G,S,L,P,R,A,L,G,F,L,N,Y,Q,V,R,A,K,M,G,A,P,A,E,-,-,A,G,G,R,L,A,P,E,R,E,H,S,Y,A,R,P,R,G,A,I,N,Y,G,T,T,P,E,A,M,L,R,P,P,S,P,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +align13;UniRef90_O56869:-,R,N,P,G,P,P,A,L,V,S,A,S,F,L,A,K,N,A,L,T,E,L,Q,F,A,D,W,D,K,I,Q,H,V,L,K,T,I,N,I,D,I,F,S,C,V,P,V,G,E,N,G,L,C,N,M,D,W,F,S,L,D,T,E,K,I,W,T,L,M,D,S,G,T,P,N,V,S,P,N,L,L,I,T,P,G,P,P,-,-,P,E,C,I,K,T,P,E,E,A,P,A,Y,F,E,A,I,S,N,Y,F,E,S,V,L,A,A,R,E,A,E,Y,A,K,L,L,A,E,Y,A,K,S,L,A,K,Y,I,R,H,K,S,Q,K,V,G,R,-,-,G,L,R,A,L,E,L,D,T,E,E,A,K,K,R,L,M,K,S,E,Y,Y,K,G,I,E,K,L,L,I,I,F,L,V,H,L,V,L,N,A,C,R,D,V,A,R,I,I,W,V,Q,Q,R,D,S,S,S,V,L,Q,K,V,T,Y,R,W,E,S,-,Q,Q,L,H,C,I,F,Q,P,L,L,V,S,P,G,P,V,F,L,D,N,D,P,L,P,L,Q,T,L,Q,H,V,N,Y,V,R,Y,L,L,G,V,P,V,L,R,F,S,M,I,E,E,S,P,S,A,Q,Y,I,P,-,-,-,-,Y,D,K,T,A,P,S,A,Y,D,V,L,A,T,I,A,R,-,-,-,-,T,C,L,T,S,S,G,C,S,R,A,S,H,D,H,T,Y,A,R,D,N,E,K,P,N,Y,S,S,S,R,I,V,L,L,A,D,S,A,L,D,T,P,-,-,-,-,-,-,-,-,-,-,-,-,-, + +jnetpred:-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,-,-,-,-,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,E,E,E,E,E,E,E,-,-,-,H,-,H,H,E,E,-,-,-,-,E,E,-,-,-,-,E,E,E,E,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,H,H,H,-,-,-,-,-,E,E,E,E,E,-,-,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, +JNETCONF:9,9,8,8,8,8,8,7,7,6,3,6,8,8,9,9,9,9,8,7,4,4,7,8,8,8,7,4,6,8,8,9,9,9,9,9,8,5,4,2,3,2,2,2,3,2,3,5,6,6,5,1,0,1,2,2,2,4,0,5,7,6,1,6,8,8,8,7,6,3,2,3,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,4,1,0,2,3,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,8,7,3,2,1,4,1,1,1,5,7,7,7,7,5,1,7,8,9,9,9,9,9,9,9,9,9,8,5,4,6,8,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,8,6,1,1,1,4,4,5,5,2,1,3,5,4,5,6,4,4,6,3,0,1,1,1,1,1,1,3,4,5,1,1,2,5,6,4,5,7,7,5,3,6,8,7,7,6,5,4,1,0,0,1,1,1,0,4,3,2,1,0,5,7,5,1,1,1,1,1,0,0,1,7,8,7,7,5,2,1,0,3,6,7,6,5,6,7,7,6,2,1,2,6,6,8,9,9,9,9,8,8,7,5,1,0,2,4,6,7,7,7,7,7,6,7,7,7,7,7,7,6,4,1,4,6,7,7,7,7,7,7,7,6,5,1,0,3,3,3,2,1,6,7,7,7,7,6,5,4,4,5,7,7,7,7,6,3,3,4,2,6, 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diff --git a/binaries/src/jpred/tests/res_d16vpa_.profile b/binaries/src/jpred/tests/res_d16vpa_.profile new file mode 100644 index 0000000..8e097f6 --- /dev/null +++ b/binaries/src/jpred/tests/res_d16vpa_.profile @@ -0,0 +1,365 @@ + +Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts + A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V + 1 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -2 -2 -1 4 1 -3 -2 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00 0.00 + 2 R -1 6 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00 0.00 + 3 M -2 -2 -3 -4 -2 -2 -3 -4 -3 1 4 -2 5 0 -3 -2 -1 -2 -1 1 0 0 0 0 0 0 0 0 0 0 50 0 50 0 0 0 0 0 0 0 0.46 0.07 + 4 P -1 -3 -3 -2 -3 -2 -2 -3 -3 -3 -4 -2 -3 -4 8 -1 -2 -4 -4 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 2.20 0.13 + 5 S 1 -1 0 -1 -1 0 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -3 -2 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0.63 0.13 + 6 P -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -5 8 -2 -2 -5 -4 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 2.29 0.21 + 7 P -2 -2 -2 -1 -4 -1 2 -3 -2 -4 -4 -1 -3 -5 8 -1 -2 -4 -4 -3 0 0 0 0 0 0 19 0 0 0 0 0 0 0 81 0 0 0 0 0 1.76 0.21 + 8 M 1 3 -2 -3 -3 0 -1 -2 -2 -2 -1 3 4 -2 -3 -1 -2 7 -1 -2 19 17 0 0 0 0 0 0 0 0 0 27 20 0 0 0 0 17 0 0 0.46 0.21 + 9 P 2 -2 -2 -2 -1 -2 -2 -2 -2 0 -1 -2 -1 -2 4 -1 -1 -3 -2 3 28 1 1 1 0 1 1 1 0 1 2 1 0 1 21 1 1 0 1 35 0.36 0.17 + 10 V 4 -2 -2 -3 -1 -2 -2 -1 -3 -1 -2 -2 -1 -3 -2 0 2 -3 -2 2 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 20 0.44 0.21 + 11 P 0 -2 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 4 5 1 -4 -3 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 80 0 0 0 0 0.73 0.21 + 12 P -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5 9 -2 -2 -5 -4 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 2.35 0.27 + 13 A 3 -2 2 2 -2 -1 -1 1 -2 -3 -3 1 -2 -4 -2 1 1 -4 -3 -2 40 0 12 11 0 0 0 7 0 0 0 11 0 0 0 10 7 0 0 0 0.36 0.30 + 14 A 4 -3 -3 -3 -2 -2 -2 -2 -3 1 1 -2 -1 -2 -2 1 -1 -4 -3 1 56 0 0 0 0 0 0 0 0 11 12 0 0 0 0 10 0 0 0 11 0.40 0.30 + 15 L -3 -3 -5 -5 -2 -3 -4 -5 -4 1 6 -4 1 -1 -4 -4 -2 -3 -2 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0.95 0.36 + 16 F 1 -3 -3 -4 -3 -3 -3 -4 0 0 -2 -3 -2 4 -4 -2 -2 0 7 -2 15 0 0 0 0 0 0 0 0 7 0 0 0 15 0 0 0 0 62 0 0.98 0.39 + 17 N -2 0 3 1 -4 5 2 -3 -1 -4 -4 3 -2 -4 -3 -1 1 -4 -3 -4 0 0 20 8 0 32 12 0 0 0 0 21 0 0 0 0 8 0 0 0 0.61 0.41 + 18 R -3 6 3 -2 -5 3 -1 -3 -1 -4 -4 1 -3 -4 -3 -1 -2 -4 -3 -4 0 64 21 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.97 0.41 + 19 L 1 -3 -4 -5 -2 -3 -4 -4 -4 0 5 -3 4 -1 -4 -3 -2 -3 -2 0 14 0 0 0 0 0 0 0 0 0 74 0 12 0 0 0 0 0 0 0 0.72 0.41 + 20 L -3 -3 -4 -4 -3 3 -2 -5 -3 4 4 -2 0 -1 -4 -3 -2 -3 -2 0 0 0 0 0 0 21 0 0 0 30 49 0 0 0 0 0 0 0 0 0 0.59 0.41 + 21 D 1 1 1 3 -3 -1 0 0 3 -3 -1 -1 -2 -4 -3 1 2 -4 -3 -3 17 8 7 20 0 0 6 5 8 0 8 0 0 0 0 7 14 0 0 0 0.26 0.41 + 22 D -2 -2 -1 5 -5 0 6 -3 -2 -5 -5 -1 -4 -5 -3 -1 -2 -5 -4 -4 0 0 0 39 0 0 61 0 0 0 0 0 0 0 0 0 0 0 0 0 1.12 0.43 + 23 L -3 -4 -5 -5 -3 -4 -4 -5 -4 1 6 -4 1 -1 -4 -4 -2 -3 -2 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 1.04 0.43 + 24 G 0 -2 1 4 -4 2 -1 4 2 -5 -5 -2 -3 -4 -3 -1 -2 -4 -3 -4 6 0 6 28 0 14 0 39 7 0 0 0 0 0 0 0 0 0 0 0 0.68 0.43 + 25 F -4 -4 -4 -5 -4 -5 -5 -5 -3 -1 -1 -5 -1 8 -5 -4 -3 0 2 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 1.58 0.43 + 26 S 2 -3 -2 0 -3 -2 -2 0 -3 -3 -3 -2 -3 -4 5 3 1 -4 -3 0 21 0 0 6 0 0 0 6 0 0 0 0 0 0 26 27 6 0 0 7 0.57 0.43 + 27 A 1 -2 -1 4 -4 0 5 -3 -2 -4 -4 -1 -3 -5 -2 -1 -2 -5 -4 -4 13 0 0 30 0 0 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0.91 0.43 + 28 G -1 -4 -2 -3 -4 -3 -4 7 -3 -5 -5 -3 -4 -3 -4 -2 -3 6 -3 -5 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 0 0 14 0 0 1.48 0.43 + 29 P -2 -3 -2 2 -4 1 -1 -3 -3 -4 -4 -2 -4 -5 8 -2 -2 -5 -4 -4 0 0 0 13 0 9 0 0 0 0 0 0 0 0 78 0 0 0 0 0 1.85 0.46 + 30 A 4 2 -2 -2 -3 -1 0 -2 -2 -3 -3 2 -3 -4 -2 3 0 -4 -3 -2 38 13 0 0 0 0 6 0 0 0 0 13 0 0 0 25 4 0 0 0 0.48 0.46 + 31 L -1 -4 -5 -5 -3 -4 -4 -5 -4 4 5 -4 2 -1 -4 -3 -2 -3 -2 0 6 0 0 0 0 0 0 0 0 26 64 0 4 0 0 0 0 0 0 0 0.75 0.46 + 32 C -2 -3 -4 -4 5 2 -3 -4 -3 1 4 -3 0 -2 -4 -1 -2 -3 -3 -1 0 0 0 0 17 13 0 0 0 6 57 0 0 0 0 6 0 0 0 0 0.62 0.46 + 33 T 2 1 -1 -2 -3 -2 -2 0 4 -3 -3 -1 -2 0 -3 3 3 -4 -2 -2 20 11 0 0 0 0 0 6 13 0 0 0 0 4 0 23 23 0 0 0 0.40 0.46 + 34 M 2 2 -3 -4 3 -2 -3 -3 -3 2 0 0 3 -3 -3 0 -2 -4 -3 2 25 12 0 0 7 0 0 0 0 11 6 7 12 0 0 6 0 0 0 13 0.28 0.46 + 35 L -3 -3 -4 -5 -3 -3 -4 -5 -4 0 5 -3 6 -1 -4 -4 -2 -3 -2 0 0 0 0 0 0 0 0 0 0 0 69 0 31 0 0 0 0 0 0 0 0.94 0.46 + 36 D -2 -1 -1 3 -5 0 6 -3 -2 -5 -4 2 -3 -5 -2 0 -2 -5 -4 -4 0 0 0 17 0 0 64 0 0 0 0 13 0 0 0 6 0 0 0 0 0.93 0.46 + 37 T -2 4 -1 -2 -3 -1 -1 -3 -2 -3 -3 3 -2 -4 -3 0 5 -4 -3 -2 0 23 0 0 0 0 0 0 0 0 0 27 0 0 0 5 44 0 0 0 0.68 0.46 + 38 W -3 -4 -5 -5 3 -4 -4 -4 -4 2 0 -4 -1 1 -5 -4 -3 11 0 0 0 0 0 0 6 0 0 0 0 20 6 0 0 6 0 0 0 56 0 7 1.64 0.46 + 39 N -3 -2 8 0 -4 -1 -2 -2 -1 -5 -5 -1 -4 -5 -3 -1 -1 -5 -4 -4 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.50 0.46 + 40 E -2 -2 -2 -1 -4 0 5 -4 -2 2 -2 -1 1 -3 -3 -2 -2 -4 -3 2 0 0 0 0 0 0 62 0 0 13 0 0 6 0 0 0 0 0 0 19 0.69 0.46 + 41 D -3 -3 0 8 -5 -2 0 -3 -2 -5 -5 -2 -5 -5 -3 -1 -2 -6 -5 -5 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.63 0.46 + 42 L -3 -4 -5 -5 -3 -3 -4 -5 -4 3 5 -4 3 -1 -4 -4 -2 -3 -2 0 0 0 0 0 0 0 0 0 0 20 72 0 9 0 0 0 0 0 0 0 0.85 0.46 + 43 F -4 -4 -5 -5 -4 -5 -5 -5 -3 -1 -1 -5 -1 8 -5 -4 -4 0 2 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 1.62 0.46 + 44 S 0 -2 -1 -1 -2 -1 -1 -2 -2 -4 -4 -1 -3 -4 -2 6 0 -4 -3 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 1.06 0.46 + 45 A 2 -4 -4 -4 10 -4 -4 1 -4 -3 -3 -4 -3 -4 -4 -2 -2 -4 -4 -2 16 0 0 0 74 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 1.59 0.46 + 46 L -3 -4 -5 -5 -3 -4 -4 -5 -4 2 4 -4 0 5 -5 -4 -3 -2 0 2 0 0 0 0 0 0 0 0 0 10 46 0 0 30 0 0 0 0 0 13 0.72 0.46 + 47 P -2 -4 -3 -3 -4 -3 -2 -4 -4 -4 -4 -2 -4 -5 9 -2 -2 -5 -4 -4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 2.52 0.46 + 48 T 0 1 -2 -3 -3 -2 -3 1 2 2 1 -2 -1 -3 -3 -2 3 -4 -3 2 5 12 0 0 0 0 0 10 7 13 13 0 0 0 0 0 23 0 0 18 0.25 0.46 + 49 N -3 -2 7 0 -4 -1 -2 2 3 -5 -4 -2 -3 0 -4 -1 -2 -4 -2 -4 0 0 72 0 0 0 0 13 9 0 0 0 0 6 0 0 0 0 0 0 1.03 0.46 + 50 A 1 -2 -2 -1 -3 -1 4 0 -2 -2 -1 1 -2 -4 1 0 -2 -4 -3 0 12 0 0 0 0 0 38 6 0 0 6 7 0 0 5 7 0 0 0 9 0.27 0.46 + 51 D -3 -2 3 6 -4 -1 1 -3 5 -4 -4 -2 -4 -4 -3 -2 -2 -5 -2 -4 0 0 13 51 0 0 6 0 19 0 0 0 0 0 0 0 0 0 0 0 0.84 0.46 + 52 L -2 -3 -4 -4 -3 -3 -4 1 -4 1 5 -3 2 -1 -4 -3 -2 -3 -3 -1 0 0 0 0 0 0 0 13 0 6 66 0 4 0 0 0 0 0 0 0 0.54 0.46 + 53 Y -3 -3 -3 -4 -3 -3 -3 -4 0 -2 1 -3 -2 2 -4 -3 -3 1 8 -2 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 76 0 1.16 0.46 + 54 R 0 3 -2 -2 5 -1 1 -3 -2 -1 -3 1 -2 -4 -3 0 2 -4 -3 -2 6 23 0 0 13 0 12 0 0 6 0 7 0 0 0 7 15 0 0 0 0.29 0.46 + 55 E -3 1 3 3 -4 0 4 -3 5 -4 -4 -1 -3 -4 -3 -1 -2 -4 -2 -4 0 6 19 13 0 0 32 0 19 0 0 0 0 0 0 0 0 0 0 0 0.59 0.46 + 56 C 2 -3 0 -3 6 -2 -3 -3 -3 1 0 -3 5 -2 -3 -1 0 -3 -3 -1 25 0 6 0 17 0 0 0 0 9 6 0 20 0 0 0 6 0 0 0 0.36 0.46 + 57 K 1 1 -2 2 -3 -1 -1 -3 -3 0 -2 3 2 -3 -3 0 0 -4 -3 0 14 5 0 13 0 0 0 0 0 6 0 26 7 0 0 6 6 0 0 6 0.17 0.46 + 58 F -3 -4 -4 -5 -3 -3 -4 -4 -4 3 2 -4 2 3 -4 -3 -2 6 -1 2 0 0 0 0 0 0 0 0 0 19 20 0 6 17 0 0 0 13 0 13 0.52 0.46 + 59 L -3 -3 -4 -4 -3 -3 -4 -4 -3 0 5 -4 0 4 -4 -4 -3 -2 -1 -1 0 0 0 0 0 0 0 0 0 0 63 0 0 20 0 0 0 0 0 0 0.57 0.46 + 60 S 0 -2 -1 -2 -2 -1 -1 -2 -2 -3 -4 -2 -3 -3 -2 6 0 -4 -3 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 0 0 0 0 0.70 0.46 + 61 T 0 -3 -2 -3 -2 -2 -3 0 -3 -1 1 -2 -1 -3 1 -1 5 -3 -3 0 6 0 0 0 0 0 0 6 0 0 13 0 0 0 7 0 45 0 0 6 0.28 0.46 + 62 L -2 -3 1 3 3 -2 -1 -2 -2 -2 1 -2 -2 -3 -3 3 -1 -4 -3 -2 0 0 6 20 7 0 0 0 0 0 17 0 0 0 0 32 0 0 0 0 0.24 0.46 + 63 P 0 -3 -3 -3 -3 -3 -3 -3 -3 -1 -2 -2 -2 -3 6 -2 2 -4 -3 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 13 0 0 20 0.73 0.46 + 64 S -2 1 1 4 -3 -1 2 0 -2 -4 -4 -1 -3 -4 -3 3 0 -4 -3 -3 0 7 4 23 0 0 13 5 0 0 0 0 0 0 0 24 6 0 0 0 0.29 0.46 + 65 D -2 -1 -1 4 -4 0 4 -3 -2 -4 -4 2 -3 -4 -2 -2 -2 -4 -3 -4 0 0 0 31 0 0 39 0 0 0 0 13 0 0 0 0 0 0 0 0 0.61 0.46 + 66 V -2 -4 -4 -4 -2 -4 -4 -5 -4 4 0 -4 0 -2 -4 -3 -1 -4 -3 6 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 74 0.79 0.46 + 67 V 0 -4 -4 -4 -2 -4 -4 -4 -4 4 1 -4 0 -1 -4 -3 -2 6 -2 4 6 0 0 0 0 0 0 0 0 29 12 0 0 0 0 0 0 13 0 32 0.60 0.46 + 68 E 0 0 -1 3 -3 -1 3 1 -2 -3 -3 1 -3 -4 -2 -1 2 -4 -3 -1 7 5 0 17 0 0 20 11 0 0 1 10 0 0 0 1 14 0 0 6 0.24 0.42 + 69 W 3 -2 0 -3 -2 1 -2 -2 -3 -2 1 -2 -1 -2 -3 -1 -2 7 -1 -2 38 0 6 0 0 6 0 1 0 0 20 0 0 0 0 1 0 18 0 0 0.46 0.42 + 70 G 0 -3 -2 -3 -3 -2 0 3 -3 -1 0 -2 5 -2 -3 0 -2 -3 -3 1 6 0 0 0 0 0 7 27 0 0 6 0 24 0 0 6 0 0 0 13 0.29 0.42 + 71 D -2 0 -1 5 -3 -1 1 -3 -1 -3 -2 -2 -2 -2 -3 0 1 -2 4 -3 1 6 0 37 0 0 6 1 0 0 5 0 0 0 0 6 11 0 17 0 0.42 0.42 + 72 A 2 -2 2 0 -3 -1 2 -2 -2 -3 0 1 -2 -3 -2 3 -1 -4 -3 -2 24 0 10 5 0 0 13 0 0 0 11 7 0 0 0 27 0 0 0 0 0.30 0.43 + 73 Y 1 -2 2 -1 -3 -1 1 2 3 -3 -3 -2 -3 -2 1 1 1 -3 3 -3 11 0 14 0 0 0 12 14 10 0 1 0 0 0 6 10 7 0 12 0 0.31 0.43 + 74 V 0 -3 -3 -3 -2 -3 -3 -4 -4 2 1 0 -1 -3 -3 -1 4 -4 -3 3 5 0 0 0 0 0 0 0 0 10 10 6 0 0 0 0 39 0 0 30 0.47 0.46 + 75 P 0 -3 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0.11920292 0.04742587 0.11920292 0.11920292 0.04742587 0.04742587 0.04742587 0.04742587 0.11920292 0.04742587 0.01798621 0.99966465 0.26894142 0.11920292 0.01798621 0.04742587 0.04742587 +0.26894142 0.26894142 0.26894142 0.73105858 0.04742587 0.73105858 0.99330715 0.11920292 0.26894142 0.04742587 0.04742587 0.50000000 0.11920292 0.04742587 0.26894142 0.26894142 0.26894142 0.04742587 0.11920292 0.11920292 +0.26894142 0.26894142 0.26894142 0.73105858 0.11920292 0.73105858 0.98201379 0.11920292 0.26894142 0.11920292 0.11920292 0.50000000 0.11920292 0.11920292 0.26894142 0.26894142 0.26894142 0.11920292 0.11920292 0.11920292 +0.95257413 0.26894142 0.26894142 0.26894142 0.26894142 0.26894142 0.26894142 0.50000000 0.26894142 0.26894142 0.26894142 0.26894142 0.26894142 0.11920292 0.26894142 0.50000000 0.50000000 0.11920292 0.26894142 0.26894142 +0.50000000 0.11920292 0.26894142 0.26894142 0.11920292 0.26894142 0.11920292 0.98201379 0.11920292 0.11920292 0.11920292 0.26894142 0.11920292 0.11920292 0.11920292 0.26894142 0.26894142 0.11920292 0.11920292 0.11920292 +0.11920292 0.11920292 0.01798621 0.01798621 0.26894142 0.11920292 0.04742587 0.01798621 0.04742587 0.88079708 0.98201379 0.04742587 0.88079708 0.50000000 0.04742587 0.04742587 0.26894142 0.11920292 0.26894142 0.73105858 +0.98201379 0.11920292 0.11920292 0.11920292 0.50000000 0.26894142 0.26894142 0.50000000 0.11920292 0.26894142 0.11920292 0.26894142 0.26894142 0.11920292 0.26894142 0.73105858 0.50000000 0.04742587 0.11920292 0.50000000 +0.98201379 0.11920292 0.11920292 0.11920292 0.50000000 0.26894142 0.26894142 0.50000000 0.11920292 0.26894142 0.11920292 0.26894142 0.26894142 0.11920292 0.26894142 0.73105858 0.50000000 0.04742587 0.11920292 0.50000000 +0.26894142 0.11920292 0.11920292 0.11920292 0.04742587 0.26894142 0.26894142 0.11920292 0.11920292 0.04742587 0.04742587 0.26894142 0.04742587 0.01798621 0.99966465 0.26894142 0.26894142 0.01798621 0.04742587 0.04742587 +0.11920292 0.99752738 0.26894142 0.11920292 0.01798621 0.73105858 0.50000000 0.04742587 0.50000000 0.04742587 0.11920292 0.88079708 0.11920292 0.04742587 0.11920292 0.26894142 0.26894142 0.04742587 0.11920292 0.04742587 +0.11920292 0.11920292 0.01798621 0.01798621 0.26894142 0.11920292 0.04742587 0.01798621 0.04742587 0.88079708 0.98201379 0.04742587 0.88079708 0.50000000 0.04742587 0.04742587 0.26894142 0.11920292 0.26894142 0.73105858 +0.73105858 0.26894142 0.73105858 0.50000000 0.26894142 0.50000000 0.50000000 0.50000000 0.26894142 0.04742587 0.04742587 0.50000000 0.11920292 0.04742587 0.26894142 0.98201379 0.88079708 0.04742587 0.11920292 0.11920292 +0.11920292 0.04742587 0.04742587 0.01798621 0.04742587 0.01798621 0.01798621 0.04742587 0.26894142 0.50000000 0.50000000 0.04742587 0.50000000 0.99908895 0.01798621 0.04742587 0.11920292 0.73105858 0.95257413 0.26894142 +0.11920292 0.11920292 0.01798621 0.01798621 0.26894142 0.11920292 0.04742587 0.01798621 0.04742587 0.88079708 0.98201379 0.04742587 0.88079708 0.50000000 0.04742587 0.04742587 0.26894142 0.11920292 0.26894142 0.73105858 diff --git a/binaries/src/jpred/tests/res_d16vpa_.res b/binaries/src/jpred/tests/res_d16vpa_.res new file mode 100644 index 0000000..55507ce --- /dev/null +++ b/binaries/src/jpred/tests/res_d16vpa_.res @@ -0,0 +1,114 @@ +>jnetpred +-----------HHHHHHHHHH-------HHHHHHHHHHHHHHH-------------EE----HHHHHHHHH- +------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH +H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------EEEEEEE--- +H-HHEE----EE----EEEE--------HHHHH--HHH-----EEEEE---------E----------HHHH +HHHHHHHHHHHH------------------------------HHHHH--------------------- +>JNETSOL25 +--------B-BB-BBB--BB--B-B--B--BB-BB--B-BBBBBBBBBB--BBBBB-BBBBBB--BB-BB-- +-BB---BBBB-B-B---B--BB-----B--BB--B--BB---B-BBB--BB-BBB-BBBBBB-BB---B--- +B--B-B------B--BB-BBB---BB-BBB-BBBBBBBBBBBBBBBBBBBBBBB-B-----BBBBB-B-B-- +---B-BBBBBBBBBBBBBBB---BB-B--B--B-BBB--B-BBBBBB-BB------BB--B-B-B-BBBBBB +BBBBBBBBBB-BBB-B--------B--BBBBB----BBBBBBBBBBB-BB---BB--B-BBB--B--- +>JNETSOL5 +--------------BB--B--------B--BB--B------BB-BB------B--B-BB------B---B-- +---------B-----------------B--BB--B-------B------B--BB--BB-BBB--B---B--- +-----B----------B---B-------B--BB-BB-B---B-BB--BB--B---------BB--B-B---- +---B-BBB-B-BB--BBB-B-------------------B-B-BB-B-B------------------B-B-B +-B---B---B-B-----------------------------B--BBB--------------------- +>JNETSOL0 +------------------B-------------------------B--------------------B------ +---------------------------------------------------------B-B----B------- +-------------------------------------B---B--B--B------------------------ +-----B-----------------------------------------------------------------B +-------------------------------------------------------------------- +>JNETHMM +-----------HHHHHHHHHH-------HHHHHHHHHHHHHHH--------HHH---E----HHHHHHHHH- +----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH +H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------EEEEEEE--- +---EEE----EE----EEEE--------HHHHH--HH------EEEEEEEE-----------------HHHH +HHHHHHHHHHHH-----------------------------HHHHHH--------------------- +>JNETPSSM +-----------HHHHHHHHHH-------HHHHHHHHHH-----------------EEE----HHHHHHHHH- +------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- +---------HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----EEEEEEE--H +HHHHHHHE---EE---EEEE---------H----HHHHH----HHHHHH-------EEE----------HHH +HHHHHHHHHHH-H-----------------------------HEEEE-----------------EE-- +>QUERY +SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA +YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL +HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES +WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG +YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL +>UniRef90_Q00028 +-----PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD +SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ +LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ +RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG +FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA-------------- +>UniRef90_Q8B635 +-----PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN +SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS +IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH +RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG +FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA-------------- +>UniRef90_Q9E205 +-----PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS +ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS +SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE +NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG +FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS-------------- +>UniRef90_Q88530 +--LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE +NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L +NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ +GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG +YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS-------------- +>UniRef90_B4XS08 +------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S +EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG +VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ +YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG +FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP------------- +>UniRef90_P09265 +---PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S +TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT +TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE +RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG +FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE----------- +>UniRef90_Q2QBC8 +------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA +HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL +HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ +ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG +YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL------------------- +>UniRef90_Q90603 +---------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK +NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD +LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ +ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV +YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD---------------- +>UniRef90_O89246 +--------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE +EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP +SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ +LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA +YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR---- +>UniRef90_Q5PP87 +----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA +PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD +-------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ +ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG +YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG---------------------------- +>UniRef90_Q65819 +----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL +AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T +AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ +RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG +FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS--------------- +>UniRef90_O56869 +-RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS +GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV +GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES +-QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA +YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP------------- diff --git a/binaries/src/jpred/tests/todo.bash b/binaries/src/jpred/tests/todo.bash index 5a757ba..030ea8a 100755 --- a/binaries/src/jpred/tests/todo.bash +++ b/binaries/src/jpred/tests/todo.bash @@ -21,9 +21,9 @@ ln -s /data/UNIREFdb databases #################################################################################################### -../jpred.pl -seq d16vpa_.fas -o res_d16vpa_ -dbname ported_db -ncpu 4 -debug -../jpred.pl -seq SCOP175B_nr.seq -o res_SCOP175B_nr -dbname ported_db -ncpu 4 -debug -../jpred.pl -seq T-state1.fas -o res_T-state1.res -dbname ported_db -ncpu 4 -debug -../jpred.pl -seq T-state2.fas -o res_T-state2.res -dbname ported_db -ncpu 4 -debug +../jpred.pl -seq d16vpa_.fas -o res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug +../jpred.pl -seq SCOP175B_nr.seq -o res_SCOP175B_nr -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug +../jpred.pl -seq T-state1.fas -o res_T-state1.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug +../jpred.pl -seq T-state2.fas -o res_T-state2.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug ./webscripts/fasta2concise < d16vpa_.res.align > d16vpa_.res.align.csv -- 1.7.10.2