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Randomizer

Download Fully Functional BioToolKit 300
(Randomizer included in BioToolKit)

Randomizer is designed to generate random DNA or protein sequences. Some of the applications are: generates control sequences for DNA-protein binding (gel-shift); generates control templates for qualitative PCR (real-time PCR); generates control sequences for testing gene-prediction and protein structure analysis.

Random DNA Sequences Generates a random DNA sequence with default or user defined nucleotide frequencies. Use setup to change the frequencies. The frequencies may be in arbitrary unit. Don't change the order of ACGT.

Random Peptide Sequences Generates a random DNA sequence with default or user defined nucleotide frequencies. The frequencies may be in arbitrary unit. Don't change the order of amino acids.

The default setup is for human proteins, i.e., the amino acid usage frequencies are from human. The frequencies can be calculated directly from the codon-usage table for any other species. Find the codon-usage table in the following format from the Codon Usage Database (http://www.kazusa.or.jp/codon/) and copy the data table into the setup input window, and then click on "OK." The amino acid usage frequencies will be calculated automatically and the results appear in the input window.

UUU F 0.46 17.1 (374332)  UCU S 0.18 14.7 (323470)  UAU Y 0.44 12.1 (264652)  UGU C 0.45 10.1 (221863)
UUC F 0.54 20.4 (448127)  UCC S 0.22 17.5 (384476)  UAC Y 0.56 15.5 (339473)  UGC C 0.55 12.4 (271056)
UUA L 0.07  7.3 (160731)  UCA S 0.15 11.9 (260418)  UAA * 0.28  0.8 ( 16884)  UGA * 0.50  1.4 ( 30111)
UUG L 0.13 12.7 (277774)  UCG S 0.06  4.5 ( 98166)  UAG * 0.22  0.6 ( 12911)  UGG W 1.00 13.0 (284246)

CUU L 0.13 12.9 (283480)  CCU P 0.28 17.3 (380219)  CAU H 0.41 10.6 (231860)  CGU R 0.08  4.7 (102673)
CUC L 0.20 19.5 (428574)  CCC P 0.33 20.0 (439256)  CAC H 0.59 15.0 (329569)  CGC R 0.19 10.8 (236986)
CUA L 0.07  7.0 (153837)  CCA P 0.27 16.7 (367297)  CAA Q 0.26 11.9 (261063)  CGA R 0.11  6.3 (138297)
CUG L 0.40 40.1 (880072)  CCG P 0.11  7.0 (154028)  CAG Q 0.74 34.4 (755209)  CGG R 0.21 11.8 (257761)

AUU I 0.36 15.8 (346233)  ACU T 0.24 12.9 (283671)  AAU N 0.46 16.7 (365457)  AGU S 0.15 12.0 (263279)
AUC I 0.48 21.3 (466577)  ACC T 0.36 19.1 (419213)  AAC N 0.54 19.3 (422697)  AGC S 0.24 19.4 (424788)
AUA I 0.16  7.2 (157385)  ACA T 0.28 14.9 (325763)  AAA K 0.42 24.0 (526117)  AGA R 0.21 11.7 (255681)
AUG M 1.00 22.3 (489160)  ACG T 0.12  6.2 (135294)  AAG K 0.58 32.5 (713826)  AGG R 0.20 11.6 (254743)

GUU V 0.18 10.9 (239795)  GCU A 0.26 18.6 (408931)  GAU D 0.46 22.1 (484271)  GGU G 0.16 10.8 (237026)
GUC V 0.24 14.6 (320190)  GCC A 0.40 28.4 (622538)  GAC D 0.54 25.7 (563848)  GGC G 0.34 22.6 (495700)
GUA V 0.11  7.0 (154102)  GCA A 0.23 16.0 (350382)  GAA E 0.42 29.0 (634985)  GGA G 0.25 16.4 (358824)
GUG V 0.47 28.7 (630151)  GCG A 0.11  7.6 (165700)  GAG E 0.58 40.3 (884368)  GGG G 0.25 16.4 (360728)

Randomize Input Sequences Constructs a sequence by drawing randomly bases from the input sequences.

Shuffling Input Sequences A random fragment of the input sequence is moved to the end of the sequence each shuffling.

Mutations Introduces user defined number of mutations. The frequencies for the bases mutated to match that for the input sequences. Back mutation is allowed.


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