- Sequence Stats - Number of sequence elements, dimers, trimers, CGs, TATAs, etc.
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Input: D/RNA sequence; desired analysis.
Action: Calculates the length of a sequence
and the occurrence of all nucleotides, di-nucleotides,
tri-nucleotides, and/or quatruple-nucleotides contained
in the input sequence. (Changes U to T for RNA sequences.)
Output: Original sequence and lists of counts. Includes hyperlinks to show potential start codons (ATG), stop codons (TAA, TAG, TGA), TATA-sequences, and polyA-signals (AATAAA, ATTAAA)
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Paste your sequence into the window and select a program for analysis
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- Text Stats - Number of words in a text
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Input: text in standard roman alphabet; any language.
Action: Calculates the total number of words
and the occurrence of single words.
Output: list of word counts.
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Paste your text into the window and select "Submit"
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- Sequence Clipper - Number of restriction sites in DNA sequence
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Input: D/RNA Sequence.
Action: Identifies restriction sites for common restriction endonucleases.
Output: Original sequence and restriction sites. (Changes U to T for RNA sequences.)
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Paste your sequence into the large window and enter a restriction enzyme to search for
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- Sequence Translator/ORF Finder
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Input: D/RNA Sequence; output type.
Action: Translates sequence into amino acid sequence or ORFs. Points out start and stop codons.
Output: Original sequence, start and stop codons, translation. (Changes U to T for RNA sequences.)
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Paste your sequence into the window and select what output you wish to see.
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- Random Sequence Generator - Generate a random DNA sequence
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Input: A number between 1 and 100,000
Action: Calculates a random sequence consisting of the four elements A, C, T, and G. The length of the sequence is defined by the user-entered number.
Output: Random DNA sequence.
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Write the desired sequence length into the window (between
1 and 100000 nucleotides) and select "run" to generate a random DNA sequence
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- Random Text Generator - Generate a random letter sequence
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Input: A number between 1 and 100,000
Action: Calculates a random sequence consisting of the 26 letters of the English alphabet. The length of the sequence is defined by the user-entered number.
Output: Random letter sequence.
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Write the desired sequence length into the window (between
1 and 100000 letters) and select "run" to generate a random letter sequence
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- Dotplot Generator - Identify repeats and palindromes
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Input: DNA, RNA, or amino acid sequences, plain text. (Start out by pasting the same sequence into both windows, plotting the sequence against itself!)
Action: Plots sequences against each other, denoting identical elements.
Output: Dotplot.
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Paste your sequences into the two windows and select "run". In order to keep the runtime at a reasonable level, please limit yourself to strings that are less than 200 elements long.
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- Sequence Permutator - Generate the complementary, reverse complementary, or reverse sequence of a DNA sequence; converts RNA to DNA
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Input: DNA or RNA sequence; desired transformation.
Action: Reverses DNA sequences, or calculates the complementary or reverse complementary to these sequences. Outputs RNA as DNA sequence.
Output: Original and transformed sequence. (Changes U to T for RNA sequences.)
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Paste your sequence into the window and select a transformation program
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DNA is a two-stranded molecule. Each
strand is a polynucleotide composed of A (adenosine), T (thymidine), C (cytidine),
and G (guanosine) residues polymerized by "dehydration" synthesis in linear chains with specific
sequences. Each strand has polarity, such that the 5'-hydroxyl (or 5'-phospho) group of the first
nucleotide begins the strand and the 3'-hydroxyl group of the final nucleotide ends the
strand; accordingly, we say that this strand runs 5' to 3' ("Five prime to three prime") . It is also essential
to know that the two strands of DNA run antiparallel such that one strand
runs 5' → 3' while the other one runs 3' → 5'. At each nucleotide residue along
the double-stranded DNA molecule, the nucleotides are complementary. That is, A
forms two hydrogen-bonds with T; C forms three hydrogen bonds with G. In most cases
the two-stranded, antiparallel, complementary DNA molecule folds to form a helical
structure which resembles a spiral staircase. This is the reason why DNA has been
referred to as the "Double Helix".
One strand of DNA holds the information that codes for various genes; this strand
is often called the template strand or antisense strand (containing anticodons). The
other, and complementary, strand is called the coding strand or sense strand (containing
codons). Since mRNA is made from the template strand, it has the same information as
the coding strand. The table above refers to triplet nucleotide codons along the sequence
of the coding or sense strand of DNA as it runs 5' → 3'; the code for the mRNA would be
identical but for the fact that RNA contains U (uridine) rather than T.
An example of two complementary strands of DNA would be:
(5' → 3') ATGGAATTCTCGCTC (Coding, sense strand)
(3' ← 5') TACCTTAAGAGCGAG (Template, antisense strand)
(5' → 3') AUGGAAUUCUCGCUC (mRNA made from Template strand)
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Links to these tools as well as to many other tools are provided in the bar on
top of this page. Check 'Sequence Utilities' under 
above. |
