| Nombre del programa
|
Descripción (inglés)
|
| aaindexextract |
Extract data from AAINDEX
|
| abiview |
Reads ABI file and display the trace
|
| acdc |
ACD compiler
|
| acdpretty |
ACD pretty printing utility
|
| acdtable |
Creates an HTML table from an ACD file
|
| acdtrace |
ACD compiler on-screen trace
|
| acdvalid |
ACD file validation
|
| antigenic |
Finds antigenic sites in proteins
|
| backtranambig |
Back translate a protein sequence to ambiguous codons
|
| backtranseq |
Back translate a protein sequence
|
| banana |
Bending and curvature plot in B-DNA
|
| biosed |
Replace or delete sequence sections
|
| btwisted |
Calculates the twisting in a B-DNA sequence
|
| cai |
CAI codon adaptation index
|
| chaos |
Create a chaos game representation plot for a sequence
|
| charge |
Protein charge plot
|
| checktrans |
Reports STOP codons and ORF statistics of a protein
|
| chips |
Codon usage statistics
|
| cirdna |
Draws circular maps of DNA constructs
|
| codcmp |
Codon usage table comparison
|
| codcopy |
Reads and writes a codon usage table
|
| coderet |
Extract CDS, mRNA and translations from feature tables
|
| compseq |
Count composition of dimer/trimer/etc words in a sequence
|
| cons |
Creates a consensus from multiple alignments
|
| cpgplot |
Plot CpG rich areas
|
| cpgreport |
Reports all CpG rich regions
|
| cusp |
Create a codon usage table
|
| cutgextract |
Extract data from CUTG
|
| cutseq |
Removes a specified section from a sequence
|
| dan |
Calculates DNA RNA/DNA melting temperature
|
| dbiblast |
Index a BLAST database
|
| dbifasta |
Database indexing for fasta file databases
|
| dbiflat |
Index a flat file database
|
| dbigcg |
Index a GCG formatted database
|
| dbxfasta |
Database b+tree indexing for fasta file databases
|
| dbxflat |
Database b+tree indexing for flat file databases
|
| dbxgcg |
Database b+tree indexing for GCG formatted databases
|
| degapseq |
Removes gap characters from sequences
|
| descseq |
Alter the name or description of a sequence
|
| diffseq |
Find differences between nearly identical sequences
|
| digest |
Protein proteolytic enzyme or reagent cleavage digest
|
| distmat |
Creates a distance matrix from multiple alignments
|
| dotmatcher |
Displays a thresholded dotplot of two sequences
|
| dotpath |
Non-overlapping wordmatch dotplot of two sequences
|
| dottup |
Displays a wordmatch dotplot of two sequences
|
| dreg |
Regular expression search of a nucleotide sequence
|
| einverted |
Finds DNA inverted repeats
|
| embossdata |
Finds or fetches data files read by EMBOSS programs
|
| embossversion |
Writes the current EMBOSS version number
|
| emma |
Multiple alignment program - interface to ClustalW program
|
| emowse |
Protein identification by mass spectrometry
|
| entret |
Reads and writes (returns) flatfile entries
|
| epestfind |
Finds PEST motifs as potential proteolytic cleavage sites
|
| eprimer3 |
Picks PCR primers and hybridization oligos
|
| equicktandem |
Finds tandem repeats
|
| est2genome |
Align EST and genomic DNA sequences
|
| etandem |
Looks for tandem repeats in a nucleotide sequence
|
| extractfeat |
Extract features from a sequence
|
| extractseq |
Extract regions from a sequence
|
| findkm |
Find Km and Vmax for an enzyme reaction
|
| freak |
Residue/base frequency table or plot
|
| fuzznuc |
Nucleic acid pattern search
|
| fuzzpro |
Protein pattern search
|
| fuzztran |
Protein pattern search after translation
|
| garnier |
Predicts protein secondary structure
|
| geecee |
Calculates fractional GC content of nucleic acid sequences
|
| getorf |
Finds and extracts open reading frames (ORFs)
|
| helixturnhelix |
Report nucleic acid binding motifs
|
| hmoment |
Hydrophobic moment calculation
|
| iep |
Calculates the isoelectric point of a protein
|
| infoalign |
Information on a multiple sequence alignment
|
| infoseq |
Displays some simple information about sequences
|
| isochore |
Plots isochores in large DNA sequences
|
| lindna |
Draws linear maps of DNA constructs
|
| listor |
Write a list file of the logical OR of two sets of sequences
|
| makenucseq |
Creates random nucleotide sequences
|
| makeprotseq |
Creates random protein sequences
|
| marscan |
Finds MAR/SAR sites in nucleic sequences
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| maskfeat |
Mask off features of a sequence
|
| maskseq |
Mask off regions of a sequence
|
| matcher |
Finds the best local alignments between two sequences
|
| megamerger |
Merge two large overlapping nucleic acid sequences
|
| merger |
Merge two overlapping sequences
|
| msbar |
Mutate sequence beyond all recognition
|
| mwcontam |
Shows molwts that match across a set of files
|
| mwfilter |
Filter noisy molwts from mass spec output
|
| needle |
Needleman-Wunsch global alignment
|
| newcpgreport |
Report CpG rich areas
|
| newcpgseek |
Reports CpG rich regions
|
| newseq |
Type in a short new sequence
|
| noreturn |
Removes carriage return from ASCII files
|
| notseq |
Exclude a set of sequences and write out the remaining ones
|
| nthseq |
Writes one sequence from a multiple set of sequences
|
| octanol |
Displays protein hydropathy
|
| oddcomp |
Find protein sequence regions with a biased composition
|
| palindrome |
Looks for inverted repeats in a nucleotide sequence
|
| pasteseq |
Insert one sequence into another
|
| patmatdb |
Search a protein sequence with a motif
|
| patmatmotifs |
Search a PROSITE motif database with a protein sequence
|
| pepcoil |
Predicts coiled coil regions
|
| pepinfo |
Plots simple amino acid properties in parallel
|
| pepnet |
Displays proteins as a helical net
|
| pepstats |
Protein statistics
|
| pepwheel |
Shows protein sequences as helices
|
| pepwindow |
Displays protein hydropathy
|
| pepwindowall |
Displays protein hydropathy of a set of sequences
|
| plotcon |
Plot quality of conservation of a sequence alignment
|
| plotorf |
Plot potential open reading frames
|
| polydot |
Displays all-against-all dotplots of a set of sequences
|
| preg |
Regular expression search of a protein sequence
|
| prettyplot |
Displays aligned sequences, with colouring and boxing
|
| prettyseq |
Output sequence with translated ranges
|
| primersearch |
Searches DNA sequences for matches with primer pairs
|
| printsextract |
Extract data from PRINTS
|
| profit |
Scan a sequence or database with a matrix or profile
|
| prophecy |
Creates matrices/profiles from multiple alignments
|
| prophet |
Gapped alignment for profiles
|
| prosextract |
Build the PROSITE motif database for use by patmatmotifs
|
| pscan |
Scans proteins using PRINTS
|
| psiphi |
Phi and psi torsion angles from protein coordinates
|
| rebaseextract |
Extract data from REBASE
|
| recoder |
Remove restriction sites but maintain same translation
|
| redata |
Search REBASE for enzyme name, references, suppliers etc
|
| remap |
Display sequence with restriction sites, translation etc
|
| restover |
Find restriction enzymes producing specific overhang
|
| restrict |
Finds restriction enzyme cleavage sites
|
| revseq |
Reverse and complement a sequence
|
| seealso |
Finds programs sharing group names
|
| seqmatchall |
All-against-all comparison of a set of sequences
|
| seqret |
Reads and writes (returns) sequences
|
| seqretsplit |
Reads and writes (returns) sequences in individual files
|
| showalign |
Displays a multiple sequence alignment
|
| showdb |
Displays information on the currently available databases
|
| showfeat |
Show features of a sequence
|
| showorf |
Pretty output of DNA translations
|
| showseq |
Display a sequence with features, translation etc
|
| shuffleseq |
Shuffles a set of sequences maintaining composition
|
| sigcleave |
Reports protein signal cleavage sites
|
| silent |
Silent mutation restriction enzyme scan
|
| sirna |
Finds siRNA duplexes in mRNA
|
| sixpack |
Display a DNA sequence with 6-frame translation and ORFs
|
| skipseq |
Reads and writes (returns) sequences, skipping first few
|
| splitter |
Split a sequence into (overlapping) smaller sequences
|
| stretcher |
Finds the best global alignment between two sequences
|
| stssearch |
Search a DNA database for matches with a set of STS primers
|
| supermatcher |
Match large sequences against one or more other sequences
|
| syco |
Synonymous codon usage Gribskov statistic plot
|
| tcode |
Fickett TESTCODE statistic to identify protein-coding DNA
|
| textsearch |
Search sequence documentation. Slow, use SRS and Entrez!
|
| tfextract |
Extract data from TRANSFAC
|
| tfm |
Displays a program's help documentation manual
|
| tfscan |
Scans DNA sequences for transcription factors
|
| tmap |
Displays membrane spanning regions
|
| tranalign |
Align nucleic coding regions given the aligned proteins
|
| transeq |
Translate nucleic acid sequences
|
| trimest |
Trim poly-A tails off EST sequences
|
| trimseq |
Trim ambiguous bits off the ends of sequences
|
| twofeat |
Finds neighbouring pairs of features in sequences
|
| union |
Reads sequence fragments and builds one sequence
|
| vectorstrip |
Strips out DNA between a pair of vector sequences
|
| water |
Smith-Waterman local alignment
|
| whichdb |
Search all databases for an entry
|
| wobble |
Wobble base plot
|
| wordcount |
Counts words of a specified size in a DNA sequence
|
| wordmatch |
Finds all exact matches of a given size between 2 sequences
|
| wossname |
Finds programs by keywords in their one-line documentation
|
| yank |
Reads a sequence range, appends the full USA to a list file
|
