Repository revision
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: http://emboss.open-bio.org/
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 5.0.0.1 16.01
Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 5.0.0.1 16.01
Plots isochores in large DNA sequences 5.0.0.1 16.01
Back translate a protein sequence 6.6.0 16.01
Reports CpG rich region 5.0.0.1 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 5.0.0.1 16.01
CAI codon adaptation index using custom codon usage file 5.0.0 16.01
Displays protein hydropathy 5.0.0.1 16.01
Create a chaos game representation plot for a sequence 5.0.0 16.01
Find protein sequence regions with a biased composition 5.0.0.1 16.01
Protein charge plot 5.0.0.1 16.01
Looks for inverted repeats in a nucleotide sequence 5.0.0.1 16.01
Reports STOP codons and ORF statistics of a protein 5.0.0.1 16.01
Insert one sequence into another 5.0.0.1 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 5.0.0.1 16.01
Codon usage table comparison 5.0.0 16.01
Plots simple amino acid properties in parallel 5.0.0.1 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 5.0.0.1 16.01
Protein statistics 5.0.0 16.01
Plot CpG rich areas 5.0.0 16.01
Shows protein sequences as helices 5.0.0.1 16.01
Reports all CpG rich regions 5.0.0.1 16.01
Displays protein hydropathy 5.0.0.1 16.01
Create a codon usage table 5.0.0 16.01
Displays protein hydropathy of a set of sequences 5.0.0.1 16.01
Removes a specified section from a sequence 5.0.0.1 16.01
Plot quality of conservation of a sequence alignment 5.0.0.1 16.01
Calculates DNA RNA/DNA melting temperature 5.0.0.1 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 5.0.0.1 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 5.0.0.1 16.01
Displays aligned sequences, with colouring and boxing 5.0.0.1 16.01
Protein proteolytic enzyme or reagent cleavage digest 5.0.0 16.01
Output sequence with translated ranges 5.0.0.1 16.01
Displays a thresholded dotplot of two sequences 5.0.0.1 16.01
Searches DNA sequences for matches with primer pairs 5.0.0.1 16.01
Non-overlapping wordmatch dotplot of two sequences 5.0.0.1 16.01
Reverse and complement a sequence 5.0.0 16.01
Displays a wordmatch dotplot of two sequences 5.0.0.1 16.01
All-against-all comparison of a set of sequences 5.0.0.1 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 5.0.0.1 16.01
Show features of a sequence 5.0.0.1 16.01
Finds PEST motifs as potential proteolytic cleavage sites 5.0.0.1 16.01
Draws linear maps of DNA constructs 5.0.0.1 16.01
Finds tandem repeats 5.0.0.1 16.01
Shuffles a set of sequences maintaining composition 5.0.0.1 16.01
Align EST and genomic DNA sequences 5.0.0.1 16.01
Reports protein signal cleavage sites 5.0.0.1 16.01
Looks for tandem repeats in a nucleotide sequence 5.0.0.1 16.01
Mutate sequence beyond all recognition 5.0.0.1 16.01
Extract features from a sequence 5.0.0.1 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 5.0.0.1 16.01
Reads and writes sequences, skipping first few 5.0.0.1 16.01
Nucleic acid pattern search 5.0.2 16.01
Split a sequence into (overlapping) smaller sequences 5.0.0.1 16.01
Protein pattern search 5.0.0.1 16.01
Match large sequences against one or more other sequences 5.0.0.1 16.01
Protein pattern search after translation 5.0.0.1 16.01
Synonymous codon usage Gribskov statistic plot 5.0.0.1 16.01
Predicts protein secondary structure 5.0.0 16.01
Fickett TESTCODE statistic to identify protein-coding DNA 5.0.0.1 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) 5.0.0.1 16.01
Needleman-Wunsch global alignment 5.0.0.1 16.01
Report nucleic acid binding motifs 5.0.0.1 16.01
Displays membrane spanning regions 5.0.0 16.01
Hydrophobic moment calculation 5.0.0.1 16.01
Align nucleic coding regions given the aligned proteins 5.0.0 16.01
Calculates the isoelectric point of a protein 5.0.0.1 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 5.0.0.1 16.01
Mask off features of a sequence 5.0.0 16.01
Trim ambiguous bits off the ends of sequences 5.0.0.1 16.01
Mask off regions of a sequence 5.0.0 16.01
Finds neighbouring pairs of features in sequences 5.0.0.1 16.01
Finds the best local alignments between two sequences 5.0.0.1 16.01
Reads sequence fragments and builds one sequence 5.0.0 16.01
Merge two large overlapping nucleic acid sequences 5.0.0.1 16.01
Strips out DNA between a pair of vector sequences 5.0.0.1 16.01
Merge two overlapping nucleic acid sequences 5.0.0.1 16.01
Smith-Waterman local alignment 5.0.0.1 16.01
Wobble base plot 5.0.0.1 16.01
Counts words of a specified size in a DNA sequence 5.0.0.1 16.01
Finds all exact matches of a given size between 2 sequences 5.0.0.1 16.01

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