QL Secondary Structure Prediction
Using Homologues
Homologues can be in any of the following formats: FASTA (Pearson), NBRF/PIR, EMBL/SwissProt, GDE, CLUSTAL, GCG/MSF
Homologues are aligned by ClustalW with the default parameters
No more than
120
characters per line
Single-letter
residue codes
Make sure no 2 names have their first 10 characters in common
Arbitrary white spaces in between proteins
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:
Unaligned Homologous
Type in your alignment here:
>t0016; DEIGDAAKKLGDASYAFAKEVDWNNGIFLQAPGKLQPLEALKAIDKMIVM GAAADPKLLKAAAEAHHKAIGSISGPNGVTSRADWDNVNAALGRVIASVP ENMVMDVYDSVSKITDPKVPAYMKSLVNGADAEKAYEGFLAFKDVVKKSQ VTSAAGPATVPSGDKIGVAAQQLSEASYPFLKEIDWLSDVYMKPLPGVSA QQSLKAIDKMIVMGAQADGNALKAAAEAHHKAIGSIDATGVTSAADYAAV NAALGRVIASVPKSTVMDVYNAMAGVTDTSIPLNMFSKVNPLDANAAAKA FYTFKDVVQAAQ >gi|94983 MVRSGKKAVVLAAVAFCATSVVQKSHGFVPSPLRQRAAAAGAAAASAATMFAPAAFADEIGDAAKKLGDA SYAFAKEVDWNNGIFLQAPGKLQPLEALKAIDKMIVMGAAADPKLLKAAAEAHHKAIGSVSGPNGVTSRA DWDNVNAALGRVIASVPENMVMDVYDSVSKITDPKVPAYMKSLVSGADAEKAYEGFLAFKDVVKKSQVTS AAGPATVPSGDKIGVAAQQLSEASYPFLKEIDWLSDVYMKPLPGVSAQQSLKAIDKMIVMGAQADGNALK AAAEAHHKAIGSIDATGVTSAADYAAVNAALGRVIASVPKSTVMDVYNAMAGATDTSIPLNMFSKVNPLD ANAAAKAFYTFKDVVQAAQR >gi|949836 MVRSGKKAVVLATVAFCATSVVQKTCGFVPSPLRQRAAAAGAAASVATMFAPAAFADEIGDAAKTLGDAS YAFAKEVDWNNGIFLQAPGKLQPLAALKAIDKMIVMGAAADPQLLKAAAEAHHKAITTVSGANGVTSRAD WDNVNAALGRVISAVPEKMVMDVYNSVAKITDPKVPAYMNSLVNGADAEKAYAGFLAFKDVVKKNQVTSA AGPATVPSGDTIGVAAQKLSDASYPFLKQIDWLSDVYLKPLPGVSAQQSLKAIDRMIVMGAQADGNALKA AAEAHHKAIGSIDAKGVTSAADYAEVNAAIGRVVASVPKSTVMDVYKAMASVTDTGIPLNMFSKVNPLDA NAAAKAFYTFKDVVLAAQR >gi|63217 MVRGARKAIAVGVAVAVACGLQKHLNFVPGPRHAAPVAAAAASMMMAPAAFADEIGDAAKKLGDASYSFA KEVDWNNGIFLQAPGKFQPLEALKAIDKMIEMGAAADPKLLKDAAEAHHKAIGSISGPNGVTSRADWDAV NAAIGRVVASVPKAKVMAVYDSVTAITDPGVPAYMKSLVNGPDAEKAYQGFLEFKDVVEKNQVATASAPA VVPSGDKIGEAAKALSDASYPFIKDIDWLSDIYLKPLPGKTAPETLKAIDKMIVMGAKMDGNLLKAAAEA HHKAIGSIDATGVTSAADYEAVNAAIGRLVASVPKTTVMDVYNSMAGVVDSSVPNNLFSKVNPLDAVAAA KGFYTFKDVVEASQR >gi|11475 KEIDWLSDVYMKPLPGVSAQQSLKAIDKMIVMGAQADGNALKAAAEAHHKAIGSIDSTGVTSVADYAAVN AALGRVIASVPKSTVMDVYNSMAGVTDTSIPLNMFSKVNPLDANAAAKVYTFKDVVQAAQR >gi|114756 MVRSGKKAVVLAAVAFCATSVVQKSHGFVPSPLRQRAAAAGAAAASAATMFAPAAFADEIGDAAKKLGDA SYHFAKEVDWNNGIFLQAPGKLQPLEATKAIDKMIVMGAAADPKLLKAAAEAHHKAIGS >gi|80705 DEIGDAAKKLGDASYAFAKEVDCNNGIFLQAPGKFQPLEALKXIXKHXV
You can look at the
references
or the
Quadratic Logistic Algorithm
Last updated : 1/20/2000