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.

Course Announcement: 2013 CSHL Computational Genomics

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Search Proteomes/Genomes
Statistical Significance from Shuffles
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)

Comments (optional):

Other search options:
Scoring matrix:
open:
ext:
Ktup:
Statistical estimates
Output limits:Show Histogram
E():
Best E():
 
Hide Alignments

Alignment Options: Highlight similarities differences compact differences.      Tabular output

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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.