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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: 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 5.0.0.1 16.01
Strips out DNA between a pair of vector sequences 5.0.0.1 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
Counts words of a specified size in a DNA sequence 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
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 5.0.0.1 16.01
Reports all CpG rich regions 5.0.0.1 16.01
Finds the best local alignments between two sequences 5.0.0.1 16.01
Shuffles a set of sequences maintaining composition 5.0.0.1 16.01
Match large sequences against one or more other sequences 5.0.0.1 16.01
Smith-Waterman local alignment 5.0.0.1 16.01
Displays protein hydropathy 5.0.0.1 16.01
Exclude a set of sequences and write out the remaining ones 5.0.0 16.01
Mutate sequence beyond all recognition 5.0.0.1 16.01
Trim poly-A tails off EST sequences 5.0.0.1 16.01
Calculates the twisting in a B-DNA sequence 5.0.0 16.01
Residue/base frequency table or plot 5.0.0.1 16.01
Displays a thresholded dotplot of two sequences 5.0.0.1 16.01
Fickett TESTCODE statistic to identify protein-coding DNA 5.0.0.1 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 5.0.0.1 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 5.0.0.1 16.01
Extract CDS, mRNA and translations from feature tables 5.0.0 16.01
Align EST and genomic DNA sequences 5.0.0.1 16.01
Synonymous codon usage Gribskov statistic plot 5.0.0.1 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 5.0.0.1 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 5.0.0.1 16.01
Protein pattern search 5.0.0.1 16.01
Back translate a protein sequence 6.6.0 16.01
Calculates DNA RNA/DNA melting temperature 5.0.0.1 16.01
Finds all exact matches of a given size between 2 sequences 5.0.0.1 16.01
Reverse and complement a sequence 5.0.0 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
Protein proteolytic enzyme or reagent cleavage digest 5.0.0 16.01
Show features of a sequence 5.0.0.1 16.01
Merge two large overlapping nucleic acid sequences 5.0.0.1 16.01
Report nucleic acid binding motifs 5.0.0.1 16.01
Trim ambiguous bits off the ends of sequences 5.0.0.1 16.01
Finds and extracts open reading frames (ORFs) 5.0.0.1 16.01
Displays a wordmatch dotplot of two sequences 5.0.0.1 16.01
Hydrophobic moment calculation 5.0.0.1 16.01
Looks for inverted repeats in a nucleotide sequence 5.0.0.1 16.01
Align nucleic coding regions given the aligned proteins 5.0.0 16.01
Removes a specified section from a sequence 5.0.0.1 16.01
Displays protein hydropathy of a set of sequences 5.0.0.1 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 5.0.0.1 16.01
Plots isochores in large DNA sequences 5.0.0.1 16.01
Reports CpG rich region 5.0.0.1 16.01
Protein charge plot 5.0.0.1 16.01
Insert one sequence into another 5.0.0.1 16.01
Translate nucleic acid sequences 5.0.0 16.01
Searches DNA sequences for matches with primer pairs 5.0.0.1 16.01
Reports protein signal cleavage sites 5.0.0.1 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 5.0.0.1 16.01
Extract regions from a sequence 5.0.0 16.01
Non-overlapping wordmatch dotplot of two sequences 5.0.0.1 16.01
Finds tandem repeats 5.0.0.1 16.01
Report CpG rich areas 5.0.0.1 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 5.0.0.1 16.01
Plot potential open reading frames 5.0.0 16.01
Find differences between nearly identical sequences 5.0.0.1 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 5.0.0.1 16.01
Plots simple amino acid properties in parallel 5.0.0.1 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 5.0.0.1 16.01
Displays protein hydropathy 5.0.0.1 16.01
Writes one sequence from a multiple set of sequences 5.0.0.1 16.01
Reads and writes sequences, skipping first few 5.0.0.1 16.01
Calculates the isoelectric point of a protein 5.0.0.1 16.01
Bending and curvature plot in B-DNA 5.0.0 16.01
Needleman-Wunsch global alignment 5.0.0.1 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 5.0.0.1 16.01
Output sequence with translated ranges 5.0.0.1 16.01
Removes carriage return from ASCII files 5.0.0 16.01
Shows protein sequences as helices 5.0.0.1 16.01
Search sequence documentation. Slow, use SRS and Entrez! 5.0.0 16.01
Extract features from a sequence 5.0.0.1 16.01
Plot quality of conservation of a sequence alignment 5.0.0.1 16.01
Replace or delete sequence sections 5.0.0 16.01
Split a sequence into (overlapping) smaller sequences 5.0.0.1 16.01
Codon usage table comparison 5.0.0 16.01

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