 |
|
Program name |
Description |
|---|---|
|
Creates a consensus from multiple alignments |
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|
Merge two large overlapping nucleic acid sequences |
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|
Merge two overlapping nucleic acid sequences |
|
Program name |
Description |
|---|---|
|
Find differences (SNPs) between nearly identical sequences |
|
Program name |
Description |
|---|---|
|
Displays a thresholded dotplot of two sequences |
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|
Displays a non-overlapping wordmatch dotplot of two sequences |
|
|
Displays a wordmatch dotplot of two sequences |
|
|
Displays all-against-all dotplots of a set of sequences |
|
Program name |
Description |
|---|---|
|
Align EST and genomic DNA sequences |
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|
Needleman-Wunsch global alignment |
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|
Finds the best global alignment between two sequences |
|
Program name |
Description |
|---|---|
|
Finds the best local alignments between two sequences |
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|
Does an all-against-all comparison of a set of sequences |
|
|
Finds a match of a large sequence against one or more sequences |
|
|
Smith-Waterman local alignment |
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|
Finds all exact matches of a given size between 2 sequences |
|
Program name |
Description |
|---|---|
|
Multiple alignment program - interface to ClustalW program |
|
|
Information on a multiple sequence alignment |
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|
Plots the quality of conservation of a sequence alignment |
|
|
Displays aligned sequences, with colouring and boxing |
|
|
Displays a multiple sequence alignment |
|
Program name |
Description |
|---|---|
|
Reads ABI file and display the trace |
|
|
Draws circular maps of DNA constructs |
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|
Draws linear maps of DNA constructs |
|
|
Displays proteins as a helical net |
|
|
Shows protein sequences as helices |
|
|
Displays aligned sequences, with colouring and boxing |
|
|
Output sequence with translated ranges |
|
|
Display a sequence with restriction cut sites, translation etc |
|
|
seealso |
Finds programs sharing group names |
|
Displays a multiple sequence alignment |
|
|
Displays information on the currently available databases |
|
|
Show features of a sequence |
|
|
Display a sequence with features, translation etc |
|
|
textsearch |
Search sequence documentation text. SRS and Entrez are faster! |
|
Program name |
Description |
|---|---|
|
Removes a specified section from a sequence |
|
|
Removes gap characters from sequences |
|
|
Alter the name or description of a sequence |
|
|
Reads and writes (returns) flatfile entries |
|
|
Extract regions from a sequence |
|
|
Displays some simple information about sequences |
|
|
Writes a list file of the logical OR of two sets of sequences |
|
|
Mask off features of a sequence |
|
|
Mask off regions of a sequence |
|
|
Type in a short new sequence |
|
|
noreturn |
Removes carriage return from ASCII files |
|
Excludes a set of sequences and writes out the remaining ones |
|
|
Writes one sequence from a multiple set of sequences |
|
|
Insert one sequence into another |
|
|
Reverse and complement a sequence |
|
|
Reads and writes (returns) sequences |
|
|
Reads and writes (returns) a set of sequences one at a time |
|
|
Reads and writes (returns) a set of sequences all at once |
|
|
seqretsplit |
Reads and writes (returns) sequences in individual files |
|
Split a sequence into (overlapping) smaller sequences |
|
|
Trim poly-A tails off EST sequences |
|
|
Trim ambiguous bits off the ends of sequences |
|
|
Strips out DNA between a pair of vector sequences |
|
Program name |
Description |
|---|---|
|
Extract CDS, mRNA and translations from feature tables |
|
|
Mask off features of a sequence |
|
|
Show features of a sequence |
|
Program name |
Description |
|---|---|
|
Information on a multiple sequence alignment |
|
|
Displays some simple information about sequences |
|
|
Finds programs sharing group names |
|
|
Displays information on the currently available databases |
|
|
Search sequence documentation text. SRS and Entrez are faster! |
|
|
tfm |
Displays a program's help documentation manual |
|
wossname |
Finds programs by keywords in their one-line documentation |
Nucleic Acid Features: composition, gene-finding, motifs, primers, repeats, restriction, translation |
Program name |
Description |
|---|---|
|
Finds DNA inverted repeats |
|
Program name |
Description |
|---|---|
|
CAI codon adaptation index |
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|
Codon usage statistics |
|
|
Codon usage table comparison |
|
|
Create a codon usage table |
|
|
Synonymous codon usage Gribskov statistic plot |
|
Program name |
Description |
|---|---|
|
Bending and curvature plot in B-DNA |
|
|
Calculates the twisting in a B-DNA sequence |
|
|
Create a chaos game representation plot for a sequence |
|
|
Counts the composition of dimer/trimer/etc words in a sequence |
|
|
Calculates DNA RNA/DNA melting temperature |
|
|
Residue/base frequency table or plot |
|
|
Plots isochores in large DNA sequences |
|
|
Counts words of a specified size in a DNA sequence |
|
Program name |
Description |
|---|---|
|
Plot CpG rich areas |
|
|
Reports all CpG rich regions |
|
|
Calculates the fractional GC content of nucleic acid sequences |
|
|
Report CpG rich areas |
|
|
Reports CpG rich regions |
|
Program name |
Description |
|---|---|
|
Finds and extracts open reading frames (ORFs) |
|
|
Finds MAR/SAR sites in nucleic sequences |
|
|
Plot potential open reading frames |
|
|
Pretty output of DNA translations |
|
|
Wobble base plot |
|
Program name |
Description |
|---|---|
|
regular expression search of a nucleotide sequence |
|
|
Nucleic acid pattern search |
|
|
Protein pattern search after translation |
|
|
Finds MAR/SAR sites in nucleic sequences |
|
Program name |
Description |
|---|---|
|
Mutate sequence beyond all recognition |
|
|
Shuffles a set of sequences maintaining composition |
|
Program name |
Description |
|---|---|
|
Selects primers for PCR and DNA amplification |
|
|
Picks PCR primers and hybridization oligos |
|
|
Searches DNA sequences for matches with primer pairs |
|
|
Searches a DNA database for matches with a set of STS primers |
|
Program name |
Description |
|---|---|
|
Scan a sequence or database with a matrix or profile |
|
|
Creates matrices/profiles from multiple alignments |
|
|
Gapped alignment for profiles |
|
Program name |
Description |
|---|---|
|
Finds DNA inverted repeats |
|
|
Finds tandem repeats |
|
|
Looks for tandem repeats in a nucleotide sequence |
|
|
Looks for inverted repeats in a nucleotide sequence |
|
Program name |
Description |
|---|---|
|
Remove restriction sites but maintain the same translation |
|
|
Search REBASE for enzyme name, references, suppliers etc |
|
|
Display a sequence with restriction cut sites, translation etc |
|
|
Finds restriction enzymes that produce a specific overhang |
|
|
Finds restriction enzyme cleavage sites |
|
|
Display a sequence with features, translation etc |
|
|
Silent mutation restriction enzyme scan |
|
Program name |
Description |
|---|---|
|
Scans DNA sequences for transcription factors |
|
Program name |
Description |
|---|---|
|
Back translate a protein sequence |
|
|
Extract CDS, mRNA and translations from feature tables |
|
|
Plot potential open reading frames |
|
|
Output sequence with translated ranges |
|
|
Display a sequence with restriction cut sites, translation etc |
|
|
Pretty output of DNA translations |
|
|
Display a sequence with features, translation etc |
|
|
Translate nucleic acid sequences |
|
Program name |
Description |
|---|---|
|
Predicts protein secondary structure |
|
|
Report nucleic acid binding motifs |
|
|
Hydrophobic moment calculation |
|
|
Predicts coiled coil regions |
|
|
Displays proteins as a helical net |
|
|
Shows protein sequences as helices |
|
|
Displays membrane spanning regions |
|
Program name |
Description |
|---|---|
|
Generate alignments for SCOP families |
|
|
Generates a sparse protein signature |
|
Program name |
Description |
|---|---|
|
Back translate a protein sequence |
|
|
Protein charge plot |
|
|
Reports STOP codons and ORF statistics of a protein sequence |
|
|
Counts the composition of dimer/trimer/etc words in a sequence |
|
|
Protein identification by mass spectrometry |
|
|
Calculates the isoelectric point of a protein |
|
|
Displays protein hydropathy |
|
|
Plots simple amino acid properties in parallel |
|
|
Protein statistics |
|
|
Displays protein hydropathy |
|
|
Displays protein hydropathy of a set of sequences |
|
Program name |
Description |
|---|---|
|
Finds antigenic sites in proteins |
|
|
Protein proteolytic enzyme or reagent cleavage digest |
|
|
Protein pattern search |
|
|
Protein pattern search after translation |
|
|
Report nucleic acid binding motifs |
|
|
Finds protein sequence regions with a biased composition |
|
|
Search a protein sequence with a motif |
|
|
Search a PROSITE motif database with a protein sequence |
|
|
Predicts coiled coil regions |
|
|
Regular expression search of a protein sequence |
|
|
Scans proteins using PRINTS |
|
|
Reports protein signal cleavage sites |
|
Program name |
Description |
|---|---|
|
Mutate sequence beyond all recognition |
|
|
Shuffles a set of sequences maintaining composition |
Miscellaneous:Enzyme kinetics, Phylogeny, Database Utilities |
Program name |
Description |
|---|---|
|
Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot |
|
Program name |
Description |
|---|---|
|
Creates a distance matrix from multiple alignments |
|
Program name |
Description |
|---|---|
|
Reads and writes (returns) one or more sequences |
|
Program name |
Description |
|---|---|
|
cutgextract |
Extract data from CUTG |
|
Build domain coordinate files |
|
|
Converts redundant EMBL-format SCOP file to non-redundant one |
|
|
printsextract |
Extract data from PRINTS |
|
prosextract |
Builds the PROSITE motif database for patmatmotifs to search |
|
rebaseextract |
Extract data from REBASE |
|
Convert raw scodiv classification file to embl-like format |
|
|
tfextract |
Extract data from TRANSFAC |
|
Program name |
Description |
|---|---|
|
dbiblast |
Index a BLAST database |
|
dbifasta |
Index a fasta database |
|
dbiflat |
Index a flat file database |
|
dbigcg |
Index a GCG formatted database |
|
Program name |
Description |
|---|---|
|
embossdata |
Finds or fetches the data files read in by the EMBOSS programs |
|
Writes the current EMBOSS version number |
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