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Sequence Utilities and Statistics

You can manipulate and analyze your sequences to gain a deeper understanding of the physical, chemical, and biological characteristics of your data. Use a graphical user interface (GUI) with many of the sequence functions in the toolbox (seqviewer).

Sequence conversion and manipulation — The toolbox provides routines for common operations, such as converting DNA or RNA sequences to amino acid sequences, that are basic to working with nucleic acid and protein sequences (aa2int, aa2nt, dna2rna, rna2dna, int2aa, int2nt, nt2aa, nt2int, seqcomplement, seqrcomplement, seqreverse).

You can manipulate your sequence by performing an in silico digestion with restriction endonucleases (restrict) and proteases (cleave).

Sequence statistics — Determine various statistics about a sequence (aacount, basecount, codoncount, dimercount, nmercount, ntdensity, codonbias, cpgisland, oligoprop), search for specific patterns within a sequence (seqshowwords, seqwordcount), or search for open reading frames (seqshoworfs). In addition, you can create random sequences for test cases (randseq).

Sequence utilities — Determine a consensus sequence from a set of multiply aligned amino acid, nucleotide sequences (seqconsensus, or a sequence profile (seqprofile). Format a sequence for display (seqdisp) or graphically show a sequence alignment with frequency data (seqlogo).

Additional MATLAB® functions efficiently handle string operations with regular expressions (regexp, seq2regexp) to look for specific patterns in a sequence and search through a library for string matches (seqmatch).

Look for possible cleavage sites in a DNA/RNA sequence by searching for palindromes (palindromes).

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