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About HMMSTR


==== HMMSTR says ======

Those who are spamming this server will be blacklisted!!!
Sorry. Please come back later.
Rosetta is provided as-is. This is a 1998 version. If you want a much higher quality prediction, try ROBETTA
Local structure predictions (HMMSTR-CM, I-sites) are still up and running.
to www.bioinfo.rpi.edu/bystrc/hmmstr/server.php
PLEASE NOTE: the new URL is minus the tilde '~'. If you have made a bookmark, update it.
Time to fix bugs is scarce. Please be patient...
Announcing I-sites2 fragment predictions, using PAIRWISE SEQUENCE COVARIANCE!!
...and introducing a nice clickable image of the Isites predictions.
Quota in effect. Please submit no more than 24 jobs per day. <--->
[ Wed May 8 12:26:45 EDT 2013 ]


Email address to which results are to be sent:

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Add a short identifying remark for this sequence:


Type or paste your amino acid sequence information below. SPECIFY INPUT FORMAT:
Single sequence: 1-letter code. from PDB coordinates.
Multiple sequence alignment file: HSSP FASTA Clustal SAF format:

Optional chain identifier:

Input options:
Use PSI-BLAST to generate multiple sequence alignment.
Use a low-complexity filter.

Output options:
A multiple sequence alignment in SAF format (only if using PSI-BLAST). example
Sequence names and weights used for generating the sequence profile. example
A set of multiple, predicted fragments sorted by confidence. example
A set of predicted backbone angles and confidences based on linking fragments. example
A one-dimensional prediction of backbone angle (phi/psi) regions based on linked fragments. example
A prediction of 3-state secondary structure, backbone angles and context symbols using HMMSTR.   example
A contact map prediction using HMMSTR-CM   example
Complete list of HMMSTR state probabilities   example
A set of 3D coordinates in PDB format, generated using ROSETTA. example

===========EXPERT SETTINGS===========

I-sites method to use: I-sites v.1 PHD + I-sites1 (example) I-sites v.2
HMMSTR model to use: C
Maximum e-value for PSI-BLAST:
Ignore I-sites shorter than in fragment prediction report.
Minimum allowed percent identity for inclusion in profile :
Minimum allowed confidence of fragment prediction:
Number of parent sequence in an input multiple alignment (usually 1) :
Create an unrefined homology-based model if possible:
Label for internal use:
Number output coordinates starting from:

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Last updated: Sun Feb 5 15:01:49 EST 2012