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)

Action

Parameters 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 0^th- or 1^st-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