Search Databases with FASTA

 This page provides searches against comprehensive databases, like SwissProt and NCBI RefSeq. The PIR1 Annotated database can be used for small, demonstration searches. The NCBI nr database is also provided, but should be your last choice for searching, because its size greatly reduces sensitivity. The best first choice for searching is a genome database from a closely related organism (e.g. RefSeq Human for vertebrates).

The Individual Proteomes/Genomes page provides searches against selected prokaryotes.

Search Proteomes/Genomes
Statistical Significance from Shuffles
Find Internal Duplications (lalign/plalign)
Hydropathy/Secondary-Structure/seg

Choose: (A) Program, (B) Query (sequence/accession), (C) Database and (D) Start Search:

(A) Program: Compare your own sequences:
(B) Query sequence:  Subset range: Use Subset range
Entrez protein sequence browser

Entrez DNA sequence browser
Protein DNA (both-strands) DNA (forward only) DNA (rev-comp only)
Upload PSSM ASN.1 file: Help with PSSMs Get PSSM from NCBI Blast RID:
(C) Database: (D) Start Search
Protein DNA
Exclude low complexity (seg)       Database size range:
Other search options:
Scoring matrix:
 open:
 ext:
 Ktup:
 Statistical estimates
Output limits:
E():
 Best E():

FASTA program information | Download FASTA | About the Author

Copyright © 1988, 2006 by William R. Pearson and the University of Virginia. All rights reserved. The FASTA program and documentation may not be sold or incorporated into a commercial product, in whole or in part, without written consent of William R. Pearson and the University of Virginia.