Search Databases with PSSMs

 This PSI-BLAST website is for demonstration purposes; it provides the same protein databases as the FASTA WWW site, and allows one to search with either PSI-BLAST or PSI-SEARCH.

For reliable BLAST searches, use the NCBI Blast web site.

FASTA Program information

Search Databases with BLAST
Search Databases with FASTA
Statistical Significance from Shuffles
Find Internal Duplications (lalign/plalign)

Choose: (A) Program, (B) Query (sequence/accession), (C.1) Multiple alignment or (C.2) PSSM ASN.1 file, (D) Database and (E) Start Search:

(A) Program:
Composition Statistics
Iterations:
E()-threshold:
(B) Query sequence: 
Entrez protein sequence browser

Entrez DNA sequence browser
Either (C.1) Multiple Alignment     Upload Multiple Alignment from File: 
Or paste in multiple alignment:

or (C.2) Multiple Alignment:

Upload PSSM ASN.1 file: Help with PSSMs
(D) Database: (E) Start Search
Protein DNA
Annotations:
Exclude low complexity (seg)
Other options:
Scoring matrix:
 open:
 ext:

Output limits:
E(): Best E():

FASTA program information | Download FASTA | About the Author

Copyright © 1996, 1997, 1998, 1999, 2002, 2014, 2015 by William R. Pearson and The Rector & Visitors of the University of Virginia
The FASTA package is open source software, licensed under the Apache License, Version 2.0 (the "License"); you may not copy this software except in compliance with the License. You may obtain a copy of the License at:
http://www.apache.org/licenses/LICENSE-2.0