Repository revision
repository tip
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository emboss_5
Name: emboss_5
Owner: devteam
Synopsis: Galaxy wrappers for EMBOSS version 5.0.0 tools
The European Molecular Biology Open Software Suite (EMBOSS) is a high quality, well documented package of open source software tools for molecular biology. It includes over 200 applications for molecular sequence analysis and other common tasks in bioinformatics.
Content homepage:
Type: unrestricted
Revision: 18:63dd26468588
This revision can be installed: True
Times cloned / installed: 7466

Contents of this repository

Name Description Version Minimum Galaxy Version
Protein pattern search after translation 16.01
Strips out DNA between a pair of vector sequences 16.01
Removes gap characters from sequences 5.0.0 16.01
Displays all-against-all dotplots of a set of sequences 16.01
Counts words of a specified size in a DNA sequence 16.01
Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 16.01
Calculates fractional GC content of nucleic acid sequences 5.0.0 16.01
Mask off features of a sequence 5.0.0 16.01
Looks for tandem repeats in a nucleotide sequence 16.01
Reports all CpG rich regions 16.01
Finds the best local alignments between two sequences 16.01
Shuffles a set of sequences maintaining composition 16.01
Match large sequences against one or more other sequences 16.01
Smith-Waterman local alignment 16.01
Displays protein hydropathy 16.01
Exclude a set of sequences and write out the remaining ones 5.0.0 16.01
Mutate sequence beyond all recognition 16.01
Trim poly-A tails off EST sequences 16.01
Calculates the twisting in a B-DNA sequence 5.0.0 16.01
Residue/base frequency table or plot 16.01
Displays a thresholded dotplot of two sequences 16.01
Fickett TESTCODE statistic to identify protein-coding DNA 16.01
Type in a short new sequence 5.0.0 16.01
Reads and writes sequences 5.0.0 16.01
Draws linear maps of DNA constructs 16.01
CAI codon adaptation index using custom codon usage file 5.0.0 16.01
Regular expression search of a nucleotide sequence 5.0.0+galaxy1 16.01
Displays aligned sequences, with colouring and boxing 16.01
Extract CDS, mRNA and translations from feature tables 5.0.0 16.01
Align EST and genomic DNA sequences 16.01
Synonymous codon usage Gribskov statistic plot 16.01
Search a protein sequence with a motif 5.0.0 16.01
Display a DNA sequence with 6-frame translation and ORFs 5.0.0+galaxy2 16.01
Wobble base plot 16.01
Create a codon usage table 5.0.0 16.01
Draws circular maps of DNA constructs 5.0.0 16.01
Finds DNA inverted repeats 16.01
Protein pattern search 16.01
Back translate a protein sequence 6.6.0 16.01
Calculates DNA RNA/DNA melting temperature 16.01
Finds all exact matches of a given size between 2 sequences 16.01
Reverse and complement a sequence 5.0.0 16.01
Predicts coiled coil regions 16.01
Reports STOP codons and ORF statistics of a protein 16.01
Protein proteolytic enzyme or reagent cleavage digest 5.0.0 16.01
Show features of a sequence 16.01
Merge two large overlapping nucleic acid sequences 16.01
Report nucleic acid binding motifs 16.01
Trim ambiguous bits off the ends of sequences 16.01
Finds and extracts open reading frames (ORFs) 16.01
Displays a wordmatch dotplot of two sequences 16.01
Hydrophobic moment calculation 16.01
Looks for inverted repeats in a nucleotide sequence 16.01
Align nucleic coding regions given the aligned proteins 5.0.0 16.01
Removes a specified section from a sequence 16.01
Displays protein hydropathy of a set of sequences 16.01
Finds siRNA duplexes in mRNA 5.0.0 16.01
Finds MAR/SAR sites in nucleic sequences 5.0.0 16.01
Count composition of dimer/trimer/etc words in a sequence 16.01
Plots isochores in large DNA sequences 16.01
Reports CpG rich region 16.01
Protein charge plot 16.01
Insert one sequence into another 16.01
Translate nucleic acid sequences 5.0.0 16.01
Searches DNA sequences for matches with primer pairs 16.01
Reports protein signal cleavage sites 16.01
Displays proteins as a helical net 5.0.0 16.01
Codon usage statistics 5.0.0 16.01
Finds PEST motifs as potential proteolytic cleavage sites 16.01
Extract regions from a sequence 5.0.0 16.01
Non-overlapping wordmatch dotplot of two sequences 16.01
Finds tandem repeats 16.01
Report CpG rich areas 16.01
Nucleic acid pattern search 5.0.3 16.01
Mask off regions of a sequence 5.0.0 16.01
Displays some simple information about sequences 5.0.0 16.01
Alter the name or description of a sequence 5.0.0 16.01
Finds neighbouring pairs of features in sequences 16.01
Plot potential open reading frames 5.0.0 16.01
Find differences between nearly identical sequences 16.01
Reads sequence fragments and builds one sequence 5.0.0 16.01
Predicts protein secondary structure 5.0.0 16.01
All-against-all comparison of a set of sequences 16.01
Plots simple amino acid properties in parallel 16.01
Plot CpG rich areas 5.0.0 16.01
CAI codon adaptation index 5.0.0 16.01
Merge two overlapping nucleic acid sequences 16.01
Displays protein hydropathy 16.01
Writes one sequence from a multiple set of sequences 16.01
Reads and writes sequences, skipping first few 16.01
Calculates the isoelectric point of a protein 16.01
Bending and curvature plot in B-DNA 5.0.0 16.01
Needleman-Wunsch global alignment 16.01
Protein statistics 5.0.0 16.01
Regular expression search of a protein sequence 5.0.0+galaxy1 16.01
Displays membrane spanning regions 5.0.0 16.01
Create a chaos game representation plot for a sequence 5.0.0 16.01
Find protein sequence regions with a biased composition 16.01
Output sequence with translated ranges 16.01
Removes carriage return from ASCII files 5.0.0 16.01
Shows protein sequences as helices 16.01
Search sequence documentation. Slow, use SRS and Entrez! 5.0.0 16.01
Extract features from a sequence 16.01
Plot quality of conservation of a sequence alignment 16.01
Replace or delete sequence sections 5.0.0 16.01
Split a sequence into (overlapping) smaller sequences 16.01
Codon usage table comparison 5.0.0 16.01

Sequence Analysis - Tools for performing Protein and DNA/RNA analysis