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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: 12:832c20329690
This revision can be installed: True
Times cloned / installed: 6591

Contents of this repository

Name Description Version Minimum Galaxy Version
Displays proteins as a helical net 5.0.0 16.01
Plot quality of conservation of a sequence alignment 16.01
Reports CpG rich region 16.01
Calculates fractional GC content of nucleic acid sequences 5.0.0 16.01
Protein proteolytic enzyme or reagent cleavage digest 5.0.0 16.01
Mask off regions of a sequence 5.0.0 16.01
Finds and extracts open reading frames (ORFs) 16.01
Fickett TESTCODE statistic to identify protein-coding DNA 16.01
Shows protein sequences as helices 16.01
Alter the name or description of a sequence 5.0.0 16.01
Replace or delete sequence sections 5.0.0 16.01
Codon usage table comparison 5.0.0 16.01
Output sequence with translated ranges 16.01
Draws linear maps of DNA constructs 16.01
Looks for tandem repeats in a nucleotide sequence 16.01
Removes carriage return from ASCII files 5.0.0 16.01
Regular expression search of a nucleotide sequence 5.0.0 16.01
Merge two large overlapping nucleic acid sequences 16.01
Create a codon usage table 5.0.0 16.01
Writes one sequence from a multiple set of sequences 16.01
Removes a specified section from a sequence 16.01
Reads and writes sequences, skipping first few 16.01
Protein pattern search 16.01
Finds DNA inverted repeats 16.01
Align nucleic coding regions given the aligned proteins 5.0.0 16.01
Hydrophobic moment calculation 16.01
Split a sequence into (overlapping) smaller sequences 16.01
Finds the best local alignments between two sequences 16.01
Bending and curvature plot in B-DNA 5.0.0 16.01
Strips out DNA between a pair of vector sequences 16.01
Report CpG rich areas 16.01
Finds MAR/SAR sites in nucleic sequences 5.0.0 16.01
Displays a thresholded dotplot of two sequences 16.01
Match large sequences against one or more other sequences 16.01
Find protein sequence regions with a biased composition 16.01
Finds neighbouring pairs of features in sequences 16.01
Finds all exact matches of a given size between 2 sequences 16.01
Calculates the twisting in a B-DNA sequence 5.0.0 16.01
All-against-all comparison of a set of sequences 16.01
Translate nucleic acid sequences 5.0.0 16.01
Shuffles a set of sequences maintaining composition 16.01
Residue/base frequency table or plot 16.01
Displays a wordmatch dotplot of two sequences 16.01
Protein pattern search after translation 16.01
CAI codon adaptation index using custom codon usage file 5.0.0 16.01
Exclude a set of sequences and write out the remaining ones 5.0.0 16.01
Plot CpG rich areas 5.0.0 16.01
Extract regions from a sequence 5.0.0 16.01
Trim poly-A tails off EST sequences 16.01
Search a protein sequence with a motif 5.0.0 16.01
Find differences between nearly identical sequences 16.01
Wobble base plot 16.01
Mutate sequence beyond all recognition 16.01
Count composition of dimer/trimer/etc words in a sequence 16.01
Extract CDS, mRNA and translations from feature tables 5.0.0 16.01
Extract features from a sequence 16.01
Type in a short new sequence 5.0.0 16.01
Displays membrane spanning regions 5.0.0 16.01
Codon usage statistics 5.0.0 16.01
Reports all CpG rich regions 16.01
Report nucleic acid binding motifs 16.01
Searches DNA sequences for matches with primer pairs 16.01
Displays aligned sequences, with colouring and boxing 16.01
CAI codon adaptation index 5.0.0 16.01
Align EST and genomic DNA sequences 16.01
Merge two overlapping nucleic acid sequences 16.01
Protein statistics 5.0.0 16.01
Smith-Waterman local alignment 16.01
Removes gap characters from sequences 5.0.0 16.01
Mask off features of a sequence 5.0.0 16.01
Finds tandem repeats 16.01
Counts words of a specified size in a DNA sequence 16.01
Finds siRNA duplexes in mRNA 5.0.0 16.01
Protein charge plot 16.01
Display a DNA sequence with 6-frame translation and ORFs 16.01
Reverse and complement a sequence 5.0.0 16.01
Trim ambiguous bits off the ends of sequences 16.01
Plots isochores in large DNA sequences 16.01
Displays protein hydropathy 16.01
Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 16.01
Nucleic acid pattern search 5.0.2 16.01
Reports protein signal cleavage sites 16.01
Show features of a sequence 16.01
Looks for inverted repeats in a nucleotide sequence 16.01
Needleman-Wunsch global alignment 16.01
Draws circular maps of DNA constructs 5.0.0 16.01
Plot potential open reading frames 5.0.0 16.01
Calculates DNA RNA/DNA melting temperature 16.01
Reads and writes sequences 5.0.0 16.01
Non-overlapping wordmatch dotplot of two sequences 16.01
Plots simple amino acid properties in parallel 16.01
Predicts protein secondary structure 5.0.0 16.01
Displays all-against-all dotplots of a set of sequences 16.01
Displays protein hydropathy 16.01
Reads sequence fragments and builds one sequence 5.0.0 16.01
Displays protein hydropathy of a set of sequences 16.01
Predicts coiled coil regions 16.01
Reports STOP codons and ORF statistics of a protein 16.01
Finds PEST motifs as potential proteolytic cleavage sites 16.01
Calculates the isoelectric point of a protein 16.01
Search sequence documentation. Slow, use SRS and Entrez! 5.0.0 16.01
Back translate a protein sequence 5.0.0 16.01
Regular expression search of a protein sequence 5.0.0 16.01
Synonymous codon usage Gribskov statistic plot 16.01
Insert one sequence into another 16.01
Displays some simple information about sequences 5.0.0 16.01
Create a chaos game representation plot for a sequence 5.0.0 16.01

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