QL Secondary Structure Prediction
Using Homologues
No more than
120
characters per line
Single-letter
residue codes
Arbitrary white spaces in between residues
Maximum of
50
homologues
Maximum of
2000
residues per protein
Gaps are represented by '
-
' (hyphens)
End gaps are automatically added to short proteins
Characters b,j,o,u,x, and z are treated as unknown residues
The following is an example of the appropriate format:
You can save the results as plain text by clicking on the link at the bottom of the results page (loading the plain text up on another page), then using the save option on your web browser
OUTPUT format:
All 3 probabilities
Predicted sec. structure
Predicted sec. structure w/ prob.
Eye-Friendly: Seq. followed by prediction in rows
INPUT format:
FASTA
Type in your alignment here:
> ty3con MDKVLNREES MELMDLLGLD RSAWGNIPVM RKAYLKKCKE LHPDKGGDED KMKRMNFLYK KMEQGVKVAH QPDFGT-WNS ---------- ---------- ----SEVPTY GTDEWESWWN TFNEKWDE-D LFCHEEMFAS D--DENT-GS Q--------- ---------- ---------- ----HSTPPK KKKKVE-DPK DFPVDLHAFL SQAVFSNR-- TVASFAVYTT KEKAQILYKK LMEKYSVTFI SRHGFGGHNI ------LFFL TPHRHRVSAI NNYCQKLCTF SFLICKGVNK EYLFYSALCR QPYAVVEESI QGGLKEHDFN PEEPEETKQV SWKLVTQYAL DTKCEDVFLL MGMYLDFQEN PLQCKKCE-- ----KKDQPN HFNHHEK-HY YNAQIFADSK NQKSICQQAV DTVAAKQRVD SIHMTREEML VERFNFLLDK MDLIFGAHGN AVLEQYMAGV AWIHCLLP-- QMDTVIYEFL KCIVLNIPKK RYWLFKGPID SGKTTLAAAL LDLCGGKSLN VNMPLERLNF ELGVGIDQFM VVFEDVKGTG AESRDLPSGH GISNLDCLRD YLDGSVKVNL ERKHQNKRTQ VFPPGIVTMN EYSVPRTLQA RFVRQIDFRP KAYLTKSLSC SEYLLEKRIL QSGMTLLLLL I--------- -------WFR PVADFAAAIH ERIVQWKERL DLEISMYTFS TMKANVGMGR PILDFPREED SEA------- ---------- -EDSGHGSST ESQSQCSSQV SEASGADTQE HCT------Y HICKGFQCFK KPKTPPPK-- - > bkvdun MDKVLNREES MELMDLLGLE RAAWGNLPLM RKAYLRKCKE FHPDKGGDED KMKRMNTLYK KMEQDVKVAH QPDFGT-WSS ---------- ---------- ----SEVPTY GTEEWESWWS SFNEKWDE-D LFCHEDMFAS D--EEATADS Q--------- ---------- ---------- ----HSTPPK KKRKVE-DPK DFPSDLHQFL SQAVFSNR-- TLACFAVYTT KEKAQILYKK LMEKYSVTFI SRHMCAGHNI ------IFFL TPHRHRVSAI NNFCQKLCTF SFLICKGVNK EYLLYSALTR DPYHTIEESI QGGLKEHDFS PEEPEETKQV SWKLITEYAV ETKCEDVFLL LGMYLEFQYN VEECKKCQ-- ----KKDQPY HFKYHEK-HF ANAIIFAESK NQKSICQQAV DTVLAKKRVD TLHMTREEML TERFNHILDK MDLIFGAHGN AVLEQYMAGV AWLHCLLP-- KMDSVIFDFL HCIVFNVPKR RYWLFKGPID SGKTTLAAGL LDLCGGKALN VNLPMERLTF ELGVAIDQYM VVFEDVKGTG AESKDLPSGH GINNLDSLRD YLDGSVKVNL EKKHLNKRTQ IFPPGLVTMN EYPVPKTLQA RFVRQIDFRP KIYLRKSLQN SEFLLEKRIL QSGMTLLLLL I--------- -------WFR PVADFATDIQ SRIVEWKERL DSEISMYTFS RMKYNICMGK CILDITREED SET------- ---------- -EDSGHGSST ESQSQCSSQV SDTSAPAEDS QRSDPHSQEL HLCKGFQCFK RPKTPPPK-- - > sv40 MDKVLNREES LQLMDLLGLE RSAWGNIPLM RKAYLKKCKE FHPDKGGDEE KMKKMNTLYK KMEDGVKYAH QPDFGGFWDA ---------- ---------- ----TEIPTY GTDEWEQWWN AFNE---E-N LFCSEEMPSS D--DEATADS Q--------- ---------- ---------- ----HSTPPK KKRKVE-DPK DFPSELLSFL SHAVFSNR-- TLACFAIYTT KEKAALLYKK IMEKYSVTFI SRHNSYNHNI ------LFFL TPHRHRVSAI NNYAQKLCTF SFLICKGVNK EYLMYSALTR DPFSVIEESL PGGLKEHDFN PEEAEETKQV SWKLVTEYAM ETKCDDVLLL LGMYLEFQYS FEMCLKCI-- ----KKEQPS HYKYHEK-HY ANAAIFADSK NQKTICQQAV DTVLAKKRVD SLQLTREQML TNRFNDLLDR MDIMFGSTGS ADIEEWMAGV AWLHCLLP-- KMDSVVYDFL KCMVYNIPKK RYWLFKGPID SGKTTLAAAL LELCGGKALN VNLPLDRLNF ELGVAIDQFL VVFEDVKGTG GESRDLPSGQ GINNLDNLRD YLDGSVKVNL EKKHLNKRTQ IFPPGIVTMN EYSVPKTLQA RFVKQIDFRP KDYLKHCLER SEFLLEKRII QSGIALLLML I--------- -------WYR PVAEFAQSIQ SRIVEWKERL DKEFSLSVYQ KMKFNVAMGI GVLDWLRNSD DDDEDSQENA DKNEDGGEKN MEDSGHETGI DSQSQGSFQA PQSSQSVHD- -----HNQPY HICRGFTCFK KPPTPPPEPE T > lpv MDQTLSKEER NELMDLLQIT RAAWGNLSMM KKAYKNVSKL YHPDKGGDSA KMQRLNELFQ RVQVTLMEIR SQCGSSSSQG YFSEDFYFGP TTFQYSPMDR DAVREDLPNP GEGSWGKWWR EFVNRQCCDD LFCSETMSSS SDEDTPPAAQ PPPPPAPSPE EEDEIEFVEE TPSSCDGSCS QSSYTCTPPK RKKTEEKKPD DFPVCLYSFL SHAIYSNK-- TMNSFLIYTS LEKARQLYKT V-EKSKIVVD FKASFSYQDE EGEGCLLFLI TLGKHRVSAV KHFCVSQCTF SFIHCKAVVK RLELYKTLSK PRFKLLEEN- KPGVSMFEF- --QEEKEQCV NWQEICNFAN EANISDVLLL LGIYIDFAVE PGKCGKCE-- ----KKQHKF HYNYH-KAHH ANACLFLESR AQKNICQQAV DQVLAAKRLK LVECSRIELL EERFLQVFDE MDDFL--HGE IEILRWMAGV AWYTILLDNC W--DVFQNMV QLITTSQRKK RNVLIKGPIN SGKTTLASAF MDFFDGKALN INCPADKLSF ELGCAIDQLC VLLDDVKGQI TLNKHLQPGQ GVNNLDNLRD HLDGTIKVNL EKKHVNKRSQ IFPPVIMTMN EYLLPRTIGV RFALHLHLKP KAYLKQSLEK SD-VVAKRIL NSGYTILLVL L--------- -------WYN PVDSFTPKVQ EKVVQWKETL EKYVSITQFG NIQQNIIDGK DPLHGIVIEE QM-------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- - > mouspol MDHQLTREES QRLMHLLKLP MEQYGNFPLM RKAFLRACKI VHPDKGGSDE LSQELISLYR RLEESLPCLS TQDFIET-DI ---------- ---------- ----LQIPSY GTPEWDEWWK EFNKDF---D LFCNEAFDRS DDEQEPQPDD SAPIILSPTY PARS------ ---------- ----QATPPK KKAKMD-SPN DMPADLMEYL SCAILSNK-- TLPCFLIYTT LEKVELLYNK LSEE---VLS PRFNQVDHKY GRKYVPIFII TGTKHRVSAV FNYCATYCSV SFIVVKGVIK EYPLYCHLCV EPYSVLQESI E-ELNSEFFD APE-DAAKNV NWVAISEYAL KINCDDIYLL MGLYKEFQSP VPNCSKCE-- ----NRMLTN HFKFH-KEHH ENAFYLQLVE NQKTICQQAV DGVIATKTVD MAQMTRNEQL AARFDKLFER LEVILSAQSS YTISMFMAGI VWFENLFPGQ SFKDLLLELL ECMVSNIPKR RYWLFTGPVN TGKTTLAAAV LDLGGTIYIS -----DCYLI ELEVANSQIH GCVEVLAEKV --KIRLPPGQ GINNLDNLRD HLDGAVKVNL EKKHLNKKTQ IFPPGIVTSN EYFIPFTLRV RFCKKLVFKF SKYQYLSLKK TECLGRYRIL QNGCTLLLLL I--------- -------YHC DLDDFAESIQ GKVRAWKERV NSEISVSTYL EMRQCCLEGR YSVCTKYSNA NTAQ------ ---------- ---------- ---------- ---------- ---------- ---------- ---------- - > bovpol --MELTSEEY EELRGLLG-- TPDIGNADTL KKAFLKACK- ---------- ---------- ---------- ---------- ---------- ---------- ------VPEY GTSQWEQWWE EFNQGFDEQD LHCDEELEPS DNEEENPAGS QAP------- --GS------ ---------- ----QATPPK KPR----TSP DFPEVLKEYV SNALFTNR-- TYNCFIIFTT AEKGKELYPC IQAAYKCTFI ALYMYNGDSV ------LYII TVGKHRVNAM ENLCSKKCTV SFLQAKGVLK PQEAYNVCC- -TFELISQNI QGGLPSSFFN PVQ-EEEKSV NWKLISEFAC SIKCTDPLLL MALYLEFTTA PEACKVCD-- ----NPRRLE HRRHHTKDHT LNALLFQDSK TQKTICNQAC DTVLAKRRLD MKTLTRNELL VQRWQGLFQE MEDLFGARGE EHLAHRMAAV MWLNALHP-- NMPDVIFNYI KMVVENKPKQ RYLLLKGPVN CGKTTVAAGL IGLCGGAYLN INCPPERLAF ELGMAIDQFT VVFEDVKGKK SSKSSLQTGI GFENLDNLRD HLDGAVPVNL ERKHQNKVTQ IFPPGIVTCN EYDIPLTVKI RMYQKVELLH NYNLYKSLKN TEEVGKKRYL QSGITWLLLL I--------- -------YFR SVDDFTEKLQ ECVVKWKERI ETEVGDMWLL TMKENIEQGK NILEK----- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- - > bfdv ------MASL RRLTELLCLP VTA--TAADI KTAYRRTALK YHPDKGGDEE KMKELNTL-- ---------- ---------- ---------- ---------- ---------- ---------- -MEEFRETEG LRADETLEDS DPEPEESG-- ---------- ---------- ---------- YATFENVSVP DIDGAFFKLM KLKKCMQTYF SVNERRKQQS CPDCHLLITS ITKMPQLKAH LYEHFGIKGH IVAHWTGIAL ------LVLQ LEKPTRISTV HNFCKKYCTI SICSVRGIKK NCV------H ALIKTLLDVP GLDLEECSID MNVVDE-KQF MHAMLYDYAV QIDCTDALLL LAIYKRLAQP TDKCPECQKD KDTVKRKRST HIDDHPR-HQ HNASLFLHIK DQKRLCQCAV DAVLAEKRFR SATMTRDERL KERFRTVLRN IQELLDGETE A-IDDFVTAI LLFNMLFPDV ---DVIVDIL QTMVKNPPKR RYYIFKGPVN TGKTTVAAAI LALCTGASLN VNGTPDRLQF ELGCAIDQFM VLFEDVKGTP EPDTNLPSGF GMVNLDNLRD HLEGSVPVNL ERKHQNKVSQ IFPPGIITMN NYVLPHTIQA RARTLVNFKH IKVYAKALRN NISVLEQRLI TKPETLLAYL LIRPESEKEI SADLRAEFLT VIENLKFEVD ERFFQYNNRL HEGLCVHE-- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- -
You can look at the
references
or the
Quadratic Logistic Algorithm
Last updated : 1/20/2000