COmparison of Multiple Protein sequence Alignments
with assessment of Statistical Significance

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
Use enhanced statistical model Yes   No  
Gap opening penalty   Gap extention penalty   Matrix
Effective length of the database Real Size   User Defined:

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



R.I. Sadreyev, M. Tang, B. Kim and N.V. Grishin (2009) COMPASS server for homology detection: improved statistical accuracy, speed, and functionality. Nucleic Acids Res doi:10.1093/nar/gkp360.
R.I. Sadreyev and N.V. Grishin (2008) Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res 36(7):2240-8.
R.I. Sadreyev and N.V. Grishin (2003) COMPASS: a tool for comparison of
multiple protein alignments with assessment of statistical significance. J Mol Biol 326(1):317-36.

Last modified: Tue Sep 9 14:38:07 CDT 2008