Protein profile Comparison with Assisting Information

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

Enter query as protein sequence or multiple alignment:

Or file name  

Choose database                 
Email address to receive the result (optional)
Job ID (optional)

Input processing options
Run PSI-BLAST if input is:   a sequence Yes   No   an alignment Yes   No
PSI-BLAST options: Iterations   E-value   Coverage   Identity
Composition-based statistics Yes   No     Low complexity filtering Yes   No
Gap fraction threshold

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

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



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