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Genome Analysis
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Nematode Analysis
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Rice-Arabidopsis comparison
Non-negative matrix factorization (NMF) for sequence analysis

Funded By
NIH

nigms

FASTA Sequence Processing Tool

Enter a set of fasta formatted sequences below.

Or upload a set of sequences from your computer:

Processing Options (top to bottom order reflects the procedure order)
ActionParameters and Comments
Select subsequence
 Start   Length   Pad Character   Anchor to 3'-end 
take a common subsequence from all sequences, anchored on either beginning or end of all sequences
Reverse Complement
None
will also reverse IUPAC characters
Dust (from NCBI)
 Window   Level   Word   Mask Char 
Removes low-complexity sequence; default values of the parameters come from NCBI
Profile Randomization
 Seed  Count   Length   Order   PseudoCounts 
builds 0th- or 1st-order stastical model of sequences entered, including any actions selected above and generates example sequences. Count and/or Length = -1 will reproduce the length distribution of the input sequences. Seed = -1:system time, Seed= 0algorithm default. Wildcard characters are ignored and not produced. Pseudocounts are an integer number added to all counts.
Circular Randomization
 Seed 
Generates random circular permutations of all sequences; Seed = -1:system time, Seed = 0: algorithm default
General Parameters
Minimum Non-ambiguous characters in processed sequence
Treat all sequences as RNA (default is DNA) 		Disallow use of wild-card (IUPAC) characters
Show verbose output