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Type the required information into the fields |
Description of field (click on description to get help) |
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Your email address [ watch typpos -:) ] |
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Password
(only for
commercial users) |
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Which type of prediction do you require? |
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Specify the format for the returned multiple-sequence alignment |
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Specify the database to be searched for similar proteins |
| PSI-BLAST
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Run iterated PSI-BLAST |
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| Output options |
| BLAST
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Return BLAST output from SWISS-PROT search |
| PHD msf
PHD rdb
PHD col
PHD casp
PHD only casp
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Return additional PHD output |
| PROF msf
PROF rdb
PROF col
PROF casp
PROF only casp
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Return additional PROF output |
| TOPITS hssp
TOPITS strip
TOPITS own
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Additional TOPITS output |
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HTML formatted results
HTML for printouts
HTML with PHD/PROF graphs
HTML with PHD/PROF graphs for printouts
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Return result in HTML (for WWW browsers) |
| Results on FTP site, NOT in email (Our current default)
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Results not sent to avoid email floods |
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keep full sequences
no PSI-BLAST
do NOT align
do NOT filter returned alignment
do NOT filter alignment used for PHD
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Process alignment |
NO ProSite
NO ProDom
NO SEG
NO COILS
NO CYSPRED
NO PredictNLS
NO PHD
NO PROF
NO ASP
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Switch off default methods
(e.g. to reduce output, or to save time) |
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| Expert options: alignment (MaxHom) |
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USE MaxHom expert options |
Tick to activate options |
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IDE = minimal % sequence identity (15 < IDE < 100)
Note: false positives rapidly increase for values < 30%! |
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Gap open penalty (1 < GO < 50) |
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Gap extension penalty (1 < GE < 50) |
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Comparison metric |
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Maximal hit value (0.5 ≤ SMAX ≤ 50) |
| Expert options: transmembrane helices (PHDhtm) |
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USE PHDhtm expert options |
Tick to activate options |
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Minimal membrane helix propensity (0 ≤ Phtm ≤ 1)
MIX = 1.0 -> strongest transmembrane helix (HTM) propensity
MIN = 0.5 -> half HTM, half not (will be labelled HTM)
MIN = 0.0 -> anything labelled HTM |
| Expert options: threading (TOPITS) |
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USE TOPITS expert options |
Tick to activate options |
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Ratio of structure:sequence (0 ≤ MIX ≤ 100)
MIX =100 -> no sequence info;
MIX = 0 -> no structure info (= pairwise alignment) |
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Number of hits reported (1 ≤ NHITS ≤ 1000) |
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Gap open penalty (1 ≤ GO ≤ 50) |
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Gap extension penalty (0.1 ≤ GE ≤ 50) |
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Comparison metric |
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Maximal hit value (0.5 ≤ SMAX ≤ 50) |
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Additional options
(see Easter Eggs) |
| Expert options: Ambivalent Sequence Predictor (ASP) |
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USE ASP expert options |
Tick to activate options |
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Window size: (1 < WS < seqLen, odd integer)
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z score cutoff: More positive Z-score cutoffs relax the significance requirement |
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minimum mu dPr score: (0 < MIN < 18, integer) |
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One-line name of protein (not necessary) |
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Specify the format of your sequence(s), alignment, or prediction |
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Either choose a file with the respective information, or ... |
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Paste, or type your sequence
- amino acids in one-letter code
- any number of white spaces allowed
- non-standard amino acids to 'X'
- use SRS6
to get your sequence from a public database
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Batch or interactive? |
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Final action |
How long to wait (status of PP queue)?
WWW services for sequence analysis
