PROCAIN
Protein profile Comparison with Assisting Information

Similarity search with alignment or sequence as a query against a database of protein families.

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Enter query as protein sequence or multiple alignment:

Or file name  

Choose database SCOP40 SCOP_TEST_SUBSET PDB70 PFAM 23.0                 
Email address to receive the result (optional)
Job ID (optional)

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Input processing options
Run PSI-BLAST if input is:   a sequence Yes   No   an alignment Yes   No
PSI-BLAST options: Iterations   E-value   Coverage 0 10 20 30 40 50 60 70 80 90 100   Identity 0 10 20 30 40 50 60 70 80 90
Composition-based statistics Yes   No     Low complexity filtering Yes   No
Gap fraction threshold 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

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Search options
Gap opening penalty   Gap extension penalty   Secondary structure score weight   Sequence motif score weight   Residue conservation score weight  

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Output formatting options
Expect   Significance threshold   Display up to hits
Top sequences to show in query   in subject 0 1
Show consensus sequences Yes   No   Show fully gapped positions Yes   No
Width of alignment segment

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Documentation

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Downloads

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Reference:
Y. Wang, R.I. Sadreyev and N.V. Grishin (2009) PROCAIN: Protein Profile Comparison with Assisting Information. Nucleic Acids Res doi:10.1093/nar/gkp212.

Last modified: Wed May 27 11:23:32 CDT 2009