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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: 16:dba489bfcd62
This revision can be installed: True
Times cloned / installed: 7457

Contents of this repository

Name Description Version Minimum Galaxy Version
Report CpG rich areas 16.01
Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 16.01
Plots isochores in large DNA sequences 16.01
Back translate a protein sequence 6.6.0 16.01
Reports CpG rich region 16.01
Bending and curvature plot in B-DNA 5.0.0 16.01
Type in a short new sequence 5.0.0 16.01
Replace or delete sequence sections 5.0.0 16.01
Removes carriage return from ASCII files 5.0.0 16.01
Calculates the twisting in a B-DNA sequence 5.0.0 16.01
Exclude a set of sequences and write out the remaining ones 5.0.0 16.01
CAI codon adaptation index 5.0.0 16.01
Writes one sequence from a multiple set of sequences 16.01
CAI codon adaptation index using custom codon usage file 5.0.0 16.01
Displays protein hydropathy 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
Protein charge plot 16.01
Looks for inverted repeats in a nucleotide sequence 16.01
Reports STOP codons and ORF statistics of a protein 16.01
Insert one sequence into another 16.01
Codon usage statistics 5.0.0 16.01
Search a protein sequence with a motif 5.0.0 16.01
Draws circular maps of DNA constructs 5.0.0 16.01
Predicts coiled coil regions 16.01
Codon usage table comparison 5.0.0 16.01
Plots simple amino acid properties in parallel 16.01
Extract CDS, mRNA and translations from feature tables 5.0.0 16.01
Displays proteins as a helical net 5.0.0 16.01
Count composition of dimer/trimer/etc words in a sequence 16.01
Protein statistics 5.0.0 16.01
Plot CpG rich areas 5.0.0 16.01
Shows protein sequences as helices 16.01
Reports all CpG rich regions 16.01
Displays protein hydropathy 16.01
Create a codon usage table 5.0.0 16.01
Displays protein hydropathy of a set of sequences 16.01
Removes a specified section from a sequence 16.01
Plot quality of conservation of a sequence alignment 16.01
Calculates DNA RNA/DNA melting temperature 16.01
Plot potential open reading frames 5.0.0 16.01
Removes gap characters from sequences 5.0.0 16.01
Displays all-against-all dotplots of a set of sequences 16.01
Alter the name or description of a sequence 5.0.0 16.01
Regular expression search of a protein sequence 5.0.0 16.01
Find differences between nearly identical sequences 16.01
Displays aligned sequences, with colouring and boxing 16.01
Protein proteolytic enzyme or reagent cleavage digest 5.0.0 16.01
Output sequence with translated ranges 16.01
Displays a thresholded dotplot of two sequences 16.01
Searches DNA sequences for matches with primer pairs 16.01
Non-overlapping wordmatch dotplot of two sequences 16.01
Reverse and complement a sequence 5.0.0 16.01
Displays a wordmatch dotplot of two sequences 16.01
All-against-all comparison of a set of sequences 16.01
Regular expression search of a nucleotide sequence 5.0.0 16.01
Reads and writes sequences 5.0.0 16.01
Finds DNA inverted repeats 16.01
Show features of a sequence 16.01
Finds PEST motifs as potential proteolytic cleavage sites 16.01
Draws linear maps of DNA constructs 16.01
Finds tandem repeats 16.01
Shuffles a set of sequences maintaining composition 16.01
Align EST and genomic DNA sequences 16.01
Reports protein signal cleavage sites 16.01
Looks for tandem repeats in a nucleotide sequence 16.01
Mutate sequence beyond all recognition 16.01
Extract features from a sequence 16.01
Finds siRNA duplexes in mRNA 5.0.0 16.01
Extract regions from a sequence 5.0.0 16.01
Display a DNA sequence with 6-frame translation and ORFs 5.0.0+galaxy2 16.01
Residue/base frequency table or plot 16.01
Reads and writes sequences, skipping first few 16.01
Nucleic acid pattern search 5.0.2 16.01
Split a sequence into (overlapping) smaller sequences 16.01
Protein pattern search 16.01
Match large sequences against one or more other sequences 16.01
Protein pattern search after translation 16.01
Synonymous codon usage Gribskov statistic plot 16.01
Predicts protein secondary structure 5.0.0 16.01
Fickett TESTCODE statistic to identify protein-coding DNA 16.01
Calculates fractional GC content of nucleic acid sequences 5.0.0 16.01
Search sequence documentation. Slow, use SRS and Entrez! 5.0.0 16.01
Finds and extracts open reading frames (ORFs) 16.01
Needleman-Wunsch global alignment 16.01
Report nucleic acid binding motifs 16.01
Displays membrane spanning regions 5.0.0 16.01
Hydrophobic moment calculation 16.01
Align nucleic coding regions given the aligned proteins 5.0.0 16.01
Calculates the isoelectric point of a protein 16.01
Translate nucleic acid sequences 5.0.0 16.01
Displays some simple information about sequences 5.0.0 16.01
Finds MAR/SAR sites in nucleic sequences 5.0.0 16.01
Trim poly-A tails off EST sequences 16.01
Mask off features of a sequence 5.0.0 16.01
Trim ambiguous bits off the ends of sequences 16.01
Mask off regions of a sequence 5.0.0 16.01
Finds neighbouring pairs of features in sequences 16.01
Finds the best local alignments between two sequences 16.01
Reads sequence fragments and builds one sequence 5.0.0 16.01
Merge two large overlapping nucleic acid sequences 16.01
Strips out DNA between a pair of vector sequences 16.01
Merge two overlapping nucleic acid sequences 16.01
Smith-Waterman local alignment 16.01
Wobble base plot 16.01
Counts words of a specified size in a DNA sequence 16.01
Finds all exact matches of a given size between 2 sequences 16.01

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