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1. Summary
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PRODRES is a fast way to obtain a Position-Specific Scoring
Matrix (PSSM) or a jackhmmer-generated profile Hidden Markov
Model (pHMM). By using the PFAM database as an
intermediate step, we can speed up the process of profile creation
by almost ten times if the query sequence has at least one hit in PFAM
domains, while, at the same time, obtaining virtually the same
profile as with a standard PSI-BLAST or jackhmmer search. If there
is no hit found PFAM domains, then a full searching in the Uniref90
database is performed.
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2. Usage
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Input to the server is an amino acid sequence in FASTA format. The users can submit your
query by either pasting one or several sequences in the text-area
provided, or, alternatively, uploading a file for batch submission of
sequences. PSSM profiles or HMMs (depending on your choices) for all
input sequences will be created.
Example input:
>sp|O93740|BACR_HALS4 Bacteriorhodopsin Halobacterium sp.
MCCAALAPPMAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITIFITTI
AAAMYFAMATGFGVTEVMVGDEALTIYWARYADWLFTTPLLLLDLSLLAGANRNTIATLI
GLDVFMIGTGAIAALSSTPGTRIAWWAISTGALLALLYVLVGTLSENARNRAPEVASLFG
RLRNLVIALWFLYPVVWILGTEGTFGILPLYWETAAFMVLDLSAKVGFGVILLQSRSVLE
RVATPTAAPT
Most common parameters for both PSI-BLAST and jackhmmer can be set
by the users accordingly in the Advanced options section
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3. Output
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Based on the choices of the Second search method, a PSSM or a pHMM will be
returned. Further, the users can also obtain raw outputs and
intermediate files by checking Keep temporary results in
the Advanced options. All
files can be downloaded as a zip archive file for further analysis.
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Furthermore, examples of results can be found here
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4. References
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PRODRES: Fast protein searches using a protein domain-reduced database.
Pascarelli S*, Tsirigos KD*, Shu N*, Peters C* and Elofsson A
[submitted to Bioinformatics]
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5. Contact
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Arne Elofsson group
Department for Biochemistry and Biophysics
The Arrhenius Laboratories for Natural Sciences
Stockholm University
SE-106 91 Stockholm, Sweden
Science for Life Laboratory
Box 1031, 17121 Solna, Sweden
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