Selected EMBOSS tools for sequence analysis
Pairwise Sequence Alignment
- Needle
-
Create an optimal global alignment of two sequences using the Needleman-Wunsch algorithm
Launch Needle
- Stretcher
-
Improved version of the Needleman-Wunsch algorithm that allows larger sequences to be globally aligned
Launch Stretcher
- Water
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Use the Smith-Waterman algorithm to calculate the local alignment of two sequences
Launch Water
- Matcher
-
Identify local similarities between two sequences using a rigorous algorithm based on the LALIGN application
Launch LALIGN
Sequence Translation
- Transeq
-
Translate nucleic acid sequences to the corresponding peptide sequences
Launch Transeq
- Sixpack
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Display DNA sequences with 6-frame translation and ORFs
Launch Sixpack
- Backtranseq
-
Back-translate protein sequences to nucleotide sequences
Launch Backtranseq
- Backtranambig
-
Back-translate protein sequences to ambiguous nucleotide sequences
Launch Backtranambig
Sequence Statistics
- Pepinfo
-
Create a variety of plots that display different amino acid properties, such as hydropathy or charged residues, and their position in the sequence
Launch Pepinfo
- Pepstats
-
Calculate properties of protein sequences such as molecular weight
Launch Pepstats
- Pepwindow
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Draw a hydropathy plot for protein sequences
Launch Pepwindow
- Cpgplot
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Identify and plot CpG islands in nucleotide sequence(s)
Launch Cpgplot
- Newcpgreport
-
Identify CpG islands in nucleotide sequence(s)
Launch Newcpgreport
- Isochore
-
Plot isochores in DNA sequences
Launch Isochore
- Dotmatcher
-
Draw a threshold dotplot of two sequences
Launch Dotmatcher
- Dotpath
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Draw a non-overlapping wordmatch dotplot of two sequences
Launch Dotpath
- Dottup
-
Display a wordmatch dotplot of two sequences
Launch Dottup
- Polydot
-
Draw dotplots for all-against-all comparison of a sequence set
Launch Polydot
Sequence Format Conversion
- Seqret
-
Read and Reformat biosequences.
Launch Seqret
The tools described on this page are provided using Search and sequence analysis tools services from EMBL-EBI in 2022
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