Selected EMBOSS tools for sequence analysis
Pairwise Sequence Alignment
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Needle
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Create an optimal global alignment of two sequences using the Needleman-Wunsch algorithm
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Stretcher
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Improved version of the Needleman-Wunsch algorithm that allows larger sequences to be globally aligned
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Water
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Use the Smith-Waterman algorithm to calculate the local alignment of two sequences
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Matcher
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Identify local similarities between two sequences using a rigorous algorithm based on the LALIGN application
Sequence Translation
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Transeq
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Translate nucleic acid sequences to the corresponding peptide sequences
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Sixpack
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Display DNA sequences with 6-frame translation and ORFs
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Backtranseq
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Back-translate protein sequences to nucleotide sequences
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Backtranambig
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Back-translate protein sequences to ambiguous nucleotide sequences
Sequence Statistics
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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
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Pepstats
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Calculate properties of protein sequences such as molecular weight
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Pepwindow
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Draw a hydropathy plot for protein sequences
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Cpgplot
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Identify and plot CpG islands in nucleotide sequence(s)
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Newcpgreport
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Identify CpG islands in nucleotide sequence(s)
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Isochore
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Plot isochores in DNA sequences
Sequence Format Conversion
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Seqret
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Read and Reformat biosequences.