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

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

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

Draw a hydropathy plot for protein sequences

Launch Pepwindow

Cpgplot

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

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 The EMBL-EBI search and sequence analysis tools APIs in 2019

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