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.

FASTA Program information

Search Databases with BLAST
Search Databases with PSI-SEARCH2
Find Internal Duplications (lalign/plalign)
Hydropathy/Secondary-Structure/seg
Retrieve result RID:
Show recent searches

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
Annotate Query Sequence (SwissProt accessions)

Upload annotation file: 
Entrez protein / Entrez DNA sequence browser
Uniprot sequence browser
Or upload query from file: 
Protein DNA (both-strands) DNA (forward only) DNA (rev-comp only)
Upload PSSM ASN.1 file: Help with PSSMs
(C) Database:      (D) Start Search
Protein DNA
Annotations:
Exclude low complexity (seg) Include isoforms
Comments (optional):
Other search options:
Scoring matrix:
 open:
 ext:
 Statistical estimates
Output limits:Max Show Histogram
E():
 Best E():
 aligns:
  Hide Alignments
 Hide Good Exons
Alignment Options: Highlight similarities differences compact differences.      Output format:

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