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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: http://emboss.open-bio.org/
Type: unrestricted
Revision: 14:2e0fb4bc860e
This revision can be installed: True
Times cloned / installed: 7742

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 5.0.0.1 16.01
Reports CpG rich region 5.0.0.1 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) 5.0.0.1 16.01
Fickett TESTCODE statistic to identify protein-coding DNA 5.0.0.1 16.01
Shows protein sequences as helices 5.0.0.1 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 5.0.0.1 16.01
Draws linear maps of DNA constructs 5.0.0.1 16.01
Looks for tandem repeats in a nucleotide sequence 5.0.0.1 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 5.0.0.1 16.01
Create a codon usage table 5.0.0 16.01
Writes one sequence from a multiple set of sequences 5.0.0.1 16.01
Removes a specified section from a sequence 5.0.0.1 16.01
Reads and writes sequences, skipping first few 5.0.0.1 16.01
Protein pattern search 5.0.0.1 16.01
Finds DNA inverted repeats 5.0.0.1 16.01
Align nucleic coding regions given the aligned proteins 5.0.0 16.01
Hydrophobic moment calculation 5.0.0.1 16.01
Split a sequence into (overlapping) smaller sequences 5.0.0.1 16.01
Finds the best local alignments between two sequences 5.0.0.1 16.01
Bending and curvature plot in B-DNA 5.0.0 16.01
Strips out DNA between a pair of vector sequences 5.0.0.1 16.01
Report CpG rich areas 5.0.0.1 16.01
Finds MAR/SAR sites in nucleic sequences 5.0.0 16.01
Displays a thresholded dotplot of two sequences 5.0.0.1 16.01
Match large sequences against one or more other sequences 5.0.0.1 16.01
Find protein sequence regions with a biased composition 5.0.0.1 16.01
Finds neighbouring pairs of features in sequences 5.0.0.1 16.01
Finds all exact matches of a given size between 2 sequences 5.0.0.1 16.01
Calculates the twisting in a B-DNA sequence 5.0.0 16.01
All-against-all comparison of a set of sequences 5.0.0.1 16.01
Translate nucleic acid sequences 5.0.0 16.01
Shuffles a set of sequences maintaining composition 5.0.0.1 16.01
Residue/base frequency table or plot 5.0.0.1 16.01
Displays a wordmatch dotplot of two sequences 5.0.0.1 16.01
Protein pattern search after translation 5.0.0.1 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 5.0.0.1 16.01
Search a protein sequence with a motif 5.0.0 16.01
Find differences between nearly identical sequences 5.0.0.1 16.01
Wobble base plot 5.0.0.1 16.01
Mutate sequence beyond all recognition 5.0.0.1 16.01
Count composition of dimer/trimer/etc words in a sequence 5.0.0.1 16.01
Extract CDS, mRNA and translations from feature tables 5.0.0 16.01
Extract features from a sequence 5.0.0.1 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 5.0.0.1 16.01
Report nucleic acid binding motifs 5.0.0.1 16.01
Searches DNA sequences for matches with primer pairs 5.0.0.1 16.01
Displays aligned sequences, with colouring and boxing 5.0.0.1 16.01
CAI codon adaptation index 5.0.0 16.01
Align EST and genomic DNA sequences 5.0.0.1 16.01
Merge two overlapping nucleic acid sequences 5.0.0.1 16.01
Protein statistics 5.0.0 16.01
Smith-Waterman local alignment 5.0.0.1 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 5.0.0.1 16.01
Counts words of a specified size in a DNA sequence 5.0.0.1 16.01
Finds siRNA duplexes in mRNA 5.0.0 16.01
Protein charge plot 5.0.0.1 16.01
Display a DNA sequence with 6-frame translation and ORFs 5.0.0+galaxy2 16.01
Reverse and complement a sequence 5.0.0 16.01
Trim ambiguous bits off the ends of sequences 5.0.0.1 16.01
Plots isochores in large DNA sequences 5.0.0.1 16.01
Displays protein hydropathy 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
Nucleic acid pattern search 5.0.2 16.01
Reports protein signal cleavage sites 5.0.0.1 16.01
Show features of a sequence 5.0.0.1 16.01
Looks for inverted repeats in a nucleotide sequence 5.0.0.1 16.01
Needleman-Wunsch global alignment 5.0.0.1 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 5.0.0.1 16.01
Reads and writes sequences 5.0.0 16.01
Non-overlapping wordmatch dotplot of two sequences 5.0.0.1 16.01
Plots simple amino acid properties in parallel 5.0.0.1 16.01
Predicts protein secondary structure 5.0.0 16.01
Displays all-against-all dotplots of a set of sequences 5.0.0.1 16.01
Displays protein hydropathy 5.0.0.1 16.01
Reads sequence fragments and builds one sequence 5.0.0 16.01
Displays protein hydropathy of a set of sequences 5.0.0.1 16.01
Predicts coiled coil regions 5.0.0.1 16.01
Reports STOP codons and ORF statistics of a protein 5.0.0.1 16.01
Finds PEST motifs as potential proteolytic cleavage sites 5.0.0.1 16.01
Calculates the isoelectric point of a protein 5.0.0.1 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 5.0.0.1 16.01
Insert one sequence into another 5.0.0.1 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

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