Format Conversion
Sequence Analysis
Sequence Figures
Random Sequences
Miscellaneous
The Sequence Manipulation Suite Copyright © 2000, 2004 Paul
Stothard. Send questions and comments to stothard@ualberta.ca
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| Sequence Manipulation Suite: |
| About |
The Sequence Manipulation Suite is written in JavaScript
1.5, which is a lightweight, cross-platform, object-oriented
scripting language. JavaScript is now standardized by the
ECMA (European Computer Manufacturers Association). The
first version of the ECMA standard is documented in the
ECMA-262 specification. The ECMA-262 standard is also
approved by the ISO (International Organization for
Standards) as ISO-16262. JavaScript 1.5 is fully compatible
with ECMA-262, Edition 3.
Sequences submitted to the Sequence Manipulation Suite do
not leave your computer and are instead manipulated by your
web browser, which executes the JavaScript. The Sequence
Manipulation Suite was written by Paul Stothard (University
of Alberta, Canada). Send questions and comments to
stothard@ualberta.ca.
Here are short descriptions of the programs that comprise
the Sequence Manipulation Suite:
Format Conversion:
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Combine FASTA - converts multiple FASTA sequence
records into a single sequence. Use Combine FASTA, for
example, when you wish to determine the codon usage for
a collection of sequences using a program that accepts a
single sequence as input.
-
EMBL to FASTA - accepts one or more EMBL files as
input and returns the DNA sequence from each in FASTA
format. Use this program when you wish to quickly remove
all of the non-DNA sequence information from an EMBL
file.
-
EMBL Feature Extractor - accepts one or more EMBL
files as input and reads the sequence feature
information described in the feature tables. The program
extracts or highlights the relevant sequence segments
and returns each sequence feature in FASTA format. EMBL
Feature Extractor is particularly helpful when you wish
to derive the sequence of a cDNA from a genomic sequence
that contains many introns.
-
EMBL Trans Extractor - accepts one or more EMBL
files as input and returns each of the protein
translations described in the files in FASTA format.
EMBL Trans Extractor can be used when you are more
interested in the predicted protein translations of a
DNA sequence than the DNA sequence itself.
-
Filter DNA - removes non-DNA characters from
text. Use this program when you wish to remove digits
and blank spaces from a sequence to make it suitable for
other applications.
-
Filter Protein - removes non-protein characters
from text. Use this program when you wish to remove
digits and blank spaces from a sequence to make it
suitable for other applications.
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GenBank to FASTA - accepts one or more GenBank
files as input and returns the entire DNA sequence from
each in FASTA format. Use this program when you wish to
quickly remove all of the non-DNA sequence information
from a GenBank file.
-
GenBank Feature Extractor - accepts one or more
GenBank files as input and reads the sequence feature
information described in the feature tables, according
to the rules outlined in the GenBank release notes. The
program extracts or highlights the relevant sequence
segments and returns each sequence feature in FASTA
format. GenBank Feature Extractor is particularly
helpful when you wish to derive the sequence of a cDNA
from a genomic sequence that contains many introns.
-
GenBank Trans Extractor - accepts one or more
GenBank files as input and returns each of the protein
translations described in the files in FASTA format.
GenBank Trans Extractor should be used when you are more
interested in the predicted protein translations of a
DNA sequence than the DNA sequence itself.
-
One to Three - converts single letter
translations to three letter translations.
-
Range Extractor DNA - accepts one or more DNA
sequences along with a set of positions or ranges. The
bases corresponding to the positions or ranges are
returned, either as a single new sequence, a set of
FASTA records, uppercase text, or lowercase text. Use
Range Extractor DNA to obtain subsequences using
position information.
-
Range Extractor Protein - accepts one or more
protein sequences along with a set of positions or
ranges. The residues corresponding to the positions or
ranges are returned, either as a single new sequence, a
set of FASTA records, uppercase text, or lowercase text.
Use Range Extractor Protein to obtain subsequences using
position information.
-
Reverse Complement - converts a DNA sequence into
its reverse, complement, or reverse-complement
counterpart. The entire IUPAC DNA alphabet is supported,
and the case of each input sequence character is
maintained. You may want to work with the
reverse-complement of a sequence if it contains an ORF
on the reverse strand.
-
Split Codons - divides a coding sequence into
three new sequences, each consisting of the bases from
one of the three codon positions.
-
Split FASTA - divides FASTA sequence records into
smaller FASTA sequences of the size you specify. An
optional overlap value can be used to create sequences
that overlap.
-
Three to One - converts three letter translations
to single letter translations. Digits and blank spaces
are removed automatically. Non-standard triplets are
ignored.
-
Window Extractor DNA - accepts one or more DNA
sequences along with a position and window size. The
bases located in the window are returned, either as a
new sequence, uppercase text, or lowercase text. Use
Window Extractor DNA to obtain subsequences using
position information.
-
Window Extractor Protein - accepts one or more
protein sequences along with a position and window size.
The residues located in the window are returned, either
as a new sequence, uppercase text, or lowercase text.
Use Window Extractor Protein to obtain subsequences
using position information.
Sequence Analysis:
-
Codon Plot - accepts a DNA sequence and generates
a graphical plot consisting of a horizontal bar for each
codon. The length of the bar is proportional to the
frequency of the codon in the codon frequency table you
enter. Use Codon Plot to find portions of DNA sequence
that may be poorly expressed, or to view a graphic
representation of a codon usage table (by using a DNA
sequence consisting of one of each codon type).
-
Codon Usage - accepts one or more DNA sequences
and returns the number and frequency of each codon type.
Since the program also compares the frequencies of
codons that code for the same amino acid (synonymous
codons), you can use it to assess whether a sequence
shows a preference for particular synonymous codons.
-
CpG Islands - reports potential CpG island
regions using the method described by
Gardiner-Garden and Frommer (1987). The calculation is performed using a 200 bp window
moving across the sequence at 1 bp intervals. CpG
islands are defined as sequence ranges where the Obs/Exp
value is greater than 0.6 and the GC content is greater
than 50%. The expected number of CpG dimers in a window
is calculated as the number of 'C's in the window
multiplied by the number of 'G's in the window, divided
by the window length. CpG islands are often found in the
5' regions of vertebrate genes, therefore this program
can be used to highlight potential genes in genomic
sequences.
-
DNA Molecular Weight - accepts one or more DNA
sequences and calculates molecular weight. Sequences can
be treated as double-stranded or single-stranded, and as
linear or circular. Use DNA Molecular Weight when
calculating molecule copy number.
-
DNA Pattern Find - accepts one or more sequences
along with a search pattern and returns the number and
positions of sites that match the pattern. The search
pattern is written as a JavaScript regular expression,
which resembles the regular expressions written in other
programming languages, such as Perl.
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DNA Stats - returns the number of occurrences of
each residue in the sequence you enter. Percentage
totals are also given for each residue, and for certain
groups of residues, allowing you to quickly compare the
results obtained for different sequences.
-
Fuzzy Search DNA - accepts a DNA sequence along
with a query sequence and returns sites that are
identical or similar to the query. You can use this
program, for example, to find sequences that can be
easily mutated into a useful restriction site.
-
Fuzzy Search Protein - accepts a protein sequence
along with a query sequence and returns sites that are
identical or similar to the query.
-
Ident and Sim - accepts a group of aligned
sequences (in FASTA or GDE format) and calculates the
identity and similarity of each sequence pair. Identity
and similarity values are often used to assess whether
or not two sequences share a common ancestor or
function.
-
Mutate for Digest - accepts a DNA sequence as
input and searches for regions that can easily be
mutated to create a restriction site of interest. The
program also reports protein translations so that you
can see which reading frames are altered by the proposed
mutations. Use Mutate for Digest to find sequences that
can be converted to a useful restriction site using PCR
or site-directed mutagenesis.
-
Multi Rev Trans - accepts a protein alignment and
uses a codon usage table to generate a degenerate DNA
coding sequence. The program also returns a graph that
can be used to find regions of minimal degeneracy at the
nucleotide level. Use Multi Rev Trans when designing PCR
primers to anneal to an unsequenced coding sequence from
a related species.
-
ORF Finder - searches for open reading frames
(ORFs) in the DNA sequence you enter. The program
returns the range of each ORF, along with its protein
translation. ORF Finder supports the entire IUPAC
alphabet and several genetic codes. Use ORF Finder to
search newly sequenced DNA for potential protein
encoding segments.
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Pairwise Align Codons - accepts two coding
sequences and determines the optimal global alignment.
Use Pairwise Align Codons to look for conserved coding
sequence regions.
-
Pairwise Align DNA - accepts two DNA sequences
and determines the optimal global alignment. Use
Pairwise Align DNA to look for conserved sequence
regions.
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Pairwise Align Protein - accepts two protein
sequences and determines the optimal global alignment.
Use Pairwise Align Protein to look for conserved
sequence regions.
-
PCR Primer Stats - accepts a list of PCR primer
sequences and returns a report describing the properties
of each primer, including melting temperature, percent
GC content, and PCR suitability. Use PCR Primer Stats to
evaluate potential PCR primers.
-
PCR Products - accepts one or more DNA sequence
templates and two primer sequences. The program searches
for perfectly matching primer annealing sites that can
generate a PCR product. Any resulting products are
sorted by size, and they are given a title specifying
their length, their position in the original sequence,
and the primers that produced them. You can use linear
or circular molecules as the template. Use PCR Products
to determine the product sizes you can expect to see
when you perform PCR in the lab.
-
Protein GRAVY - Protein GRAVY returns the GRAVY
(grand average of hydropathy) value for the protein
sequences you enter. The GRAVY value is calculated by
adding the hydropathy value for each residue and
dividing by the length of the sequence (Kyte and Doolittle; 1982).
-
Protein Isoelectric Point - calculates the
theoretical pI (isoelectric point) for the protein
sequence you enter. Use Protein Isoelectric Point when
you want to know approximately where on a 2-D gel a
particular protein will be found.
-
Protein Molecular Weight - accepts one or more
protein sequences and calculates molecular weight. You
can append copies of commonly used epitopes and fusion
proteins using the supplied list. Use Protein Molecular
Weight when you wish to predict the location of a
protein of interest on a gel in relation to a set of
protein standards.
-
Protein Pattern Find - accepts one or more
sequences along with a search pattern and returns the
number and positions of sites that match the pattern.
The search pattern is written as a JavaScript regular
expression, which resembles the regular expressions
written in other programming languages, such as Perl.
-
Protein Stats - returns the number of occurrences
of each residue in the sequence you enter. Percentage
totals are also given for each residue, and for certain
groups of residues, allowing you to quickly compare the
results obtained for different sequences.
-
Restriction Digest - cleaves a DNA sequence in a
virtual restriction digest, with one, two, or three
restriction enzymes. The resulting fragments are sorted
by size, and they are given a title specifying their
length, their position in the original sequence, and the
enzyme sites that produced them. You can digest linear
or circular molecules, and even a mixture of molecules
(by entering more than one sequence in FASTA format).
Use Restriction Digest to determine the fragment sizes
you will see when you perform a digest in the lab.
-
Restriction Summary - accepts a DNA sequence and
returns the number and positions of commonly used
restriction endonuclease cut sites. Use this program if
you wish to quickly determine whether or not an enzyme
cuts a particular segment of DNA.
-
Reverse Translate - accepts a protein sequence as
input and uses a codon usage table to generate a DNA
sequence representing the most likely non-degenerate
coding sequence. A consensus sequence derived from all
the possible codons for each amino acid is also
returned. Use Reverse Translate when designing PCR
primers to anneal to an unsequenced coding sequence from
a related species.
-
Translate - accepts a DNA sequence and converts
it into a protein in the reading frame you specify.
Translate supports the entire IUPAC alphabet and several
genetic codes.
Sequence Figures:
-
Color Align Conservation - accepts a group of
aligned sequences (in FASTA or GDE format) and colors
the alignment. The program examines each residue and
compares it to the other residues in the same column.
Residues that are identical among the sequences are
given a black background, and those that are similar
among the sequences are given a gray background. The
remaining residues receive a white background. You can
specify the percentage of residues that must be
identical and similar for the coloring to be applied.
Use Color Align Conservation to enhance the output of
sequence alignment programs.
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Color Align Properties - accepts a group of
aligned sequences (in FASTA or GDE format) and colors
the alignment. The program examines each residue and
compares it to the other residues in the same column.
Residues that are identical or similar among the
sequences are given a colored background. The color is
chosen according to the biochemical properties of the
residue. You can specify the percentage of residues that
must be identical and similar for the coloring to be
applied. Use Color Align Properties to highlight protein
regions with conserved biochemical properties.
-
Group DNA - adjusts the spacing of DNA sequences
and adds numbering. You can specify the group size (the
number of bases per group), as well as the number of
bases per line. The output of this program can serve as
a convenient reference, since the numbering and spacing
allows you to quickly locate specific bases.
-
Group Protein - adjusts the spacing of protein
sequences and adds numbering. You can specify the group
size (the number of residues per group), as well as the
number of residues per line. The output of this program
can serve as a convenient reference, since the numbering
and spacing allows you to quickly locate specific
residues.
-
Primer Map - accepts a DNA sequence and returns a
textual map showing the annealing positions of PCR
primers. Restriction endonuclease cut sites, and the
protein translations of the DNA sequence can also be
shown. Use this program to produce a useful reference
figure, particularly when you have designed a large
number of primers for a particular template. Primer Map
supports the entire IUPAC alphabet and several genetic
codes.
-
Restriction Map - accepts a DNA sequence and
returns a textual map showing the positions of
restriction endonuclease cut sites. The translation of
the DNA sequence is also given, in the reading frame you
specify. Use the output of this program as a reference
when planning cloning strategies. Restriction Map
supports the entire IUPAC alphabet and several genetic
codes.
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Translation Map - accepts a DNA sequence and
returns a textual map displaying protein translations.
The reading frame of the translation can be specified
(1, 2, 3, or all three), or you can choose to treat
uppercase text as the reading frame. Translation Map
supports the entire IUPAC alphabet and several genetic
codes.
Random Sequences:
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Mutate DNA - introduces base changes into a DNA
sequence. You can select the number of mutations to
introduce, and whether or not to preserve the first and
last three bases in the sequence, to reflect selection
acting to maintain start and stop codons. The position
of each mutation is chosen randomly, and multiple
mutations can occur at a single site. Mutated sequences
can be used to evaluate the significance of sequence
analysis results.
-
Mutate Protein - introduces residue changes into
a protein sequence. You can select the number of
mutations to introduce, and whether or not to preserve
the first residue in the sequence, to reflect selection
acting to maintain a start codon. The position of each
mutation is chosen randomly, and multiple mutations can
occur at a single site. Mutated sequences can be used to
evaluate the significance of sequence analysis results.
-
Random Coding DNA - generates a random open
reading frame beginning with a start codon and ending
with a stop codon. You can choose the genetic code to
use and the length of the sequence to generate. Random
sequences can be used to evaluate the significance of
sequence analysis results.
-
Random DNA Sequence - generates random sequences
of the length you specify. Random sequences can be used
to evaluate the significance of sequence analysis
results.
-
Random DNA Regions - replaces regions of DNA
sequences with random bases. Random sequences can be
used to evaluate the significance of sequence analysis
results.
-
Random Protein Sequence - generates random
sequences of the length you specify. Random sequences
can be used to evaluate the significance of sequence
analysis results.
-
Random Protein Regions - replaces regions of
protein sequences with random residues. Random sequences
can be used to evaluate the significance of sequence
analysis results.
-
Sample DNA - randomly selects bases from the
guide sequence until a sequence of the length you
specify is constructed. Each selected base is replaced
so that it can be selected again.
-
Sample Protein - randomly selects bases from the
guide sequence until a sequence of the length you
specify is constructed. Each selected residue is
replaced so that it can be selected again.
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Shuffle DNA - randomly shuffles a DNA sequence.
Shuffled sequences can be used to evaluate the
significance of sequence analysis results, particularly
when sequence composition is an important consideration.
-
Shuffle Protein - randomly shuffles a protein
sequence. Shuffled sequences can be used to evaluate the
significance of sequence analysis results, particularly
when sequence composition is an important consideration.
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