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redata [advanced form ][doc]
Search REBASE for enzyme name, references, suppliers etc.- restrict [advanced form ][doc]
Finds restriction enzyme cleavage sites
- silent[advanced form ][doc]
Silent mutation restriction enzyme scan
- profit[advanced form ][doc]
Scan a sequence or database with a matrix or profile
- prophecy [advanced form][doc]
Creates matrices/profiles from multiple alignments
- prophet [advanced form][doc]
Gapped alignment for profiles
- matcher [advanced form][doc]
Finds the best local alignments between two sequences
- water [advanced form][doc]
Smith-Waterman local alignment.
- emma [advanced form][doc]
Multiple alignment program - interface to ClustalW program
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chaos [advanced form][doc]
Create a chaos game representation plot for a sequence - cpgplot [advanced form][doc]
Plot CpG rich areas
- cpgreport [advanced form][doc]
Reports all CpG rich regions
- diffseq [advanced form][doc]
Find differences (SNPs) between nearly identical sequences
- dotmatcher [advanced form][doc]
Displays a thresholded dotplot of two sequences
- dotpath [advanced form][doc]
Displays a non-overlapping wordmatch dotplot of two sequences
- dottup [advanced form][doc]
Displays a wordmatch dotplot of two sequences
- einverted [advanced form][doc]
Finds DNA inverted repeats
- equicktandem [advanced form][doc]
Finds tandem repeats
- etandem [advanced form][doc]
Looks for tandem repeats in a nucleotide sequence
- isochore [advanced form][doc]
Plots isochores in large DNA sequences
- newcpgseek [advanced form][doc]
Reports CpG rich regions
- palindrome [advanced form][doc]
Looks for inverted repeats in a nucleotide sequence
- polydot [advanced form][doc]
Displays all-against-all dotplots of a set of sequences
- redata [advanced form][doc]
Search REBASE for enzyme name, references, suppliers etc.
- restrict [advanced form][doc]
Finds restriction enzyme cleavage sites
- silent [advanced form][doc]
Silent mutation restriction enzyme scan
- tfscan [advanced form][doc]
Scans DNA sequences for transcription factors
- showseq [advanced form][doc]
Display a sequence with features, translation etc..
- oddcomp [advanced form][doc]
Finds protein sequence regions with a biased composition
- cpgplot [advanced form][doc]
Plot CpG rich areas
- cpgreport [advanced form][doc]
Reports all CpG rich regions
- geecee [advanced form][doc]
Calculates the fractional GC content of nucleic acid sequences
- newcpgseek [advanced form][doc]
Reports CpG rich regions
- silent [advanced form][doc]
Silent mutation restriction enzyme scan
- octanol [advanced form][doc]
Displays protein hydropathy
- pepwindow [advanced form][doc]
Displays protein hydropathy
- pepwindowall [advanced form] [doc]
Displays protein hydropathy of a set of sequences
- syco [advanced form][doc]
Synonymous codon usage Gribskov statistic plot
- backtranseq [advanced form][doc]
Back translate a protein sequence
- cusp [advanced form][doc]
Create a codon usage table
- prettyseq [advanced form] [doc]
Output sequence with translated ranges
- showorf [advanced form][doc]
Pretty output of DNA translations
- transeq [advanced form][doc]
Translate nucleic acid sequences
- findkm [advanced form][doc]
Calculates Km and Vmax for an enzyme reaction using a Hanes/Woolf plot
- prettyplot [advanced form][doc]
Displays aligned sequences, with colouring and boxing
- wobble [advanced form][doc]
Wobble base plot
- cirdna [advanced form][doc]
Draws circular maps of DNA constructs
- lindna [advanced form][doc]
Draws linear maps of DNA constructs
- chaos [advanced form][doc]
Create a chaos game representation plot for a sequence
- chips [advanced form][doc]
Codon usage statistics
- codcmp [advanced form][doc]
Codon usage table comparison
- cusp [advanced form][doc]
Create a codon usage table
- freak [advanced form][doc]
Residue/base frequency table or plot
- geecee [advanced form][doc]
Calculates the fractional GC content of nucleic acid sequences
- isochore [advanced form][doc]
Plots isochores in large DNA sequences
- newcpgseek [advanced form][doc]
Reports CpG rich regions
- wordcount [advanced form][doc]
Counts words of a specified size in a DNA sequence
- diffseq [advanced form][doc]
Find differences (SNPs) between nearly identical sequences
- dotpath [advanced form][doc]
Displays a non-overlapping wordmatch dotplot of two sequences
- dottup [advanced form][doc]
Displays a wordmatch dotplot of two sequences
- primersearch [advanced form][doc]
Searches DNA sequences for matches with primer pairs
- cutseq [advanced form][doc]
Removes a specified section from a sequence.
- descseq [advanced form][doc]
Alter the name or description of a sequence.
- extractseq [advanced form][doc]
Extract regions from a sequence
- maskseq [advanced form][doc]
Mask off regions of a sequence.
- megamerger [advanced form][doc]
Merge two large overlapping nucleic acid sequences
- merger [advanced form][doc]
Merge two overlapping nucleic acid sequences
- newseq [advanced form][doc]
Type in a short new sequence.
- nthseq [advanced form][doc]
Writes one sequence from a multiple set of sequences
- pasteseq [advanced form][doc]
Insert one sequence into another
- revseq [advanced form][doc]
Reverse and complement a sequence
- splitter [advanced form][doc]
Split a sequence into (overlapping) smaller sequences
- trimseq [advanced form][doc]
Trim ambiguous bits off the ends of sequences
- vectorstrip [advanced form][doc
Strips out DNA between a pair of vector sequences
- chips [advanced form][doc]
Codon usage statistics
- cusp [advanced form][doc]
Create a codon usage table
- syco
[advanced form][doc]
Synonymous codon usage Gribskov statistic plot
- checktrans [advanced form][doc]
Reports STOP codons and ORF statistics of a protein sequence
- digest [advanced form][doc]
Protein proteolytic enzyme or reagent cleavage digest
- iep [advanced form][doc]
Calculates the isoelectric point of a protein
- octanol [advanced form][doc]
Displays protein hydropathy
- pepinfo [advanced form][doc]
Plots simple amino acid properties in parallel
- pepnet [advanced form][doc]
Displays proteins as a helical net
- pepstats [advanced form][doc]
Protein statistics
- pepwheel [advanced form][doc]
Shows protein sequences as helices
- pepwindow [advanced form][doc]
Displays protein hydropathy
- pepwindowall [advanced form][doc]
Displays protein hydropathy of a set of sequences
- prima [advanced form][doc]
Selects primers for PCR and DNA amplification.
- primersearch [advanced form][doc]
Searches DNA sequences for matches with primer pairs
- stssearch [advanced form][doc]
Searches a DNA database for matches with a set of STS primers
- plotorf [advanced form][doc]
Plot potential open reading frames
- dreg [advanced form][doc]
regular expression search of a nucleotide sequence
- fuzznuc [advanced form][doc]
Nucleic acid pattern search
- fuzzpro [advanced form][doc]
Protein pattern search
- fuzztran [advanced form][doc]
Protein pattern search after translation
- patmatdb [advanced form][doc]
Search a protein sequence with a motif
- patmatmotifs [advanced form][doc]
Search a PROSITE motif database with a protein sequence
- preg [advanced form][doc]
regular expression search of a protein sequence
- pscan [advanced form][doc]
Scans proteins using PRINTS
- tfscan [advanced form][doc]
Scans DNA sequences for transcription factors
- needle [advanced form][doc]
Needleman-Wunsch global alignment.
- stretcher [advanced form][doc]
Finds the best global alignment between two sequences
- prettyseq [advanced form][doc]
Output sequence with translated ranges
- showorf [advanced form][doc]
Pretty output of DNA translations
- compseq [advanced form][doc]
Counts the composition of dimer/trimer/etc words in a sequence
- tfscan [advanced form][doc]
Scans DNA sequences for transcription factors
- msbar [advanced form] [doc]
Mutate sequence beyond all recognition
- shuffleseq [advanced form][doc]
Shuffles a set of sequences maintaining composition
- helixturnhelix [advanced form][doc]
Report nucleic acid binding motifs
- patmatdb [advanced form][doc]
Search a protein sequence with a motif
- patmatmotifs [advanced form][doc]
Search a PROSITE motif database with a protein sequence
- pscan [advanced form][doc]
Scans proteins using PRINTS
- tfscan [advanced form][doc]
Scans DNA sequences for transcription factors
- banana [advanced form][doc]
Bending and curvature plot in B-DNA
- complex [advanced form][doc]
Find the linguistic complexity in nucleotide sequences
- dan [advanced form][doc]
Calculates DNA RNA/DNA melting temperature
- antigenic [advanced form][doc]
Finds antigenic sites in proteins
- diffseq [advanced form][doc]
Find differences (SNPs) between nearly identical sequences
- dotmatcher [advanced form][doc]
Displays a thresholded dotplot of two sequences
- dotpath [advanced form][doc]
Displays a non-overlapping wordmatch dotplot of two sequences
- dottup [advanced form][doc]
Displays a wordmatch dotplot of two sequences
- helixturnhelix [advanced form][doc]
Report nucleic acid binding motifs
- pepcoil [advanced form][doc]
Predicts coiled coil regions
- polydot [advanced form][doc]
Displays all-against-all dotplots of a set of sequences
- pscan [advanced form][doc]
Scans proteins using PRINTS
- sigcleave [advanced form][doc]
Reports protein signal cleavage sites
- tmap [advanced form][doc]
Displays membrane spanning regions
- einverted [advanced form][doc]
Finds DNA inverted repeats
- equicktandem [advanced form][doc]
Finds tandem repeats
- etandem [advanced form][doc]
Looks for tandem repeats in a nucleotide sequence
- palindrome [advanced form][doc]
Looks for inverted repeats in a nucleotide sequence
- dotmatcher [advanced form][doc]
Displays a thresholded dotplot of two sequences
- polydot [advanced form][doc]
Displays all-against-all dotplots of a set of sequences
- seqmatchall [advanced form][doc]
Does an all-against-all comparison of a set of sequences
- stssearch [advanced form][doc]
Searches a DNA database for matches with a set of STS primers
- supermatcher [advanced form][doc]
Finds a match of a large sequence against one or mo
re sequences
- wordmatch [advanced form][doc]
Finds all exact matches of a given size between 2 sequences
- remap [advanced form][doc]
Display a sequence with restriction cut sites, translation etc..
- getorf [advanced form][doc]
Finds and extracts open reading frames (ORFs)
- helixturnhelix [advanced form][doc]
Report nucleic acid binding motifs
- pepcoil [advanced form][doc]
Predicts coiled coil regions
- pepnet [advanced form][doc]
Displays proteins as a helical net
- pepwheel [advanced form][doc]
Shows protein sequences as helices
- sigcleave [advanced form][doc]
Reports protein signal cleavage sites
- est2genome [advanced form][doc]
Align EST and genomic DNA sequences
- megamerger [advanced form][doc]
Merge two large overlapping nucleic acid sequences
- merger [advanced form][doc]
Merge two overlapping nucleic acid sequences
- infoseq [advanced form][doc] Displays some simple information about sequences
- seqinfo [advanced form][doc]
Returns sequence information