Selected EMBOSS tools for sequence analysis
Pairwise Sequence Alignment
- Needle
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Create an optimal global alignment of two sequences using the Needleman-Wunsch algorithm
- Stretcher
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Improved version of the Needleman-Wunsch algorithm that allows larger sequences to be globally aligned
- Water
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Use the Smith-Waterman algorithm to calculate the local alignment of two sequences
- Matcher
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Identify local similarities between two sequences using a rigorous algorithm based on the LALIGN application
Sequence Translation
- Transeq
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Translate nucleic acid sequences to the corresponding peptide sequences
- Sixpack
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Display DNA sequences with 6-frame translation and ORFs
- Backtranseq
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Back-translate protein sequences to nucleotide sequences
- Backtranambig
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Back-translate protein sequences to ambiguous nucleotide sequences
Sequence Statistics
- Pepinfo
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Create a variety of plots that display different amino acid properties, such as hydropathy or charged residues, and their position in the sequence
- Pepstats
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Calculate properties of protein sequences such as molecular weight
- Pepwindow
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Draw a hydropathy plot for protein sequences
- Cpgplot
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Identify and plot CpG islands in nucleotide sequence(s)
- Newcpgreport
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Identify CpG islands in nucleotide sequence(s)
- Isochore
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Plot isochores in DNA sequences
- Dotmatcher
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Draw a threshold dotplot of two sequences
- Dotpath
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Draw a non-overlapping wordmatch dotplot of two sequences
- Dottup
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Display a wordmatch dotplot of two sequences
- Polydot
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Draw dotplots for all-against-all comparison of a sequence set
Sequence Format Conversion
- Seqret
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Read and Reformat biosequences.
The tools described on this page are provided using The EMBL-EBI search and sequence analysis tools APIs in 2019
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