Bioinformatics Toolbox

Sequence Utilities and Statistics

You can manipulate and analyze your sequence to gain a deeper understanding of your data.

Sequence 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 or protein sequences (aa2int, aa2nt, dna2rna, rna2dna, int2aa, int2nt, nt2aa, nt2int, seqcomplement, seqrcomplement, seqreverse).

Additional functions in MATLAB efficiently handle string operations with regular expressions (, seq2regexp), and look for possible cleavage sites in DNA/RNA sequences by searching for palindromes (palindromes).

Sequence statistics — You can determine various statistics about the sequences (aacount, basecount, codoncount, dimercount, nmercount, ntdensity), search for specific patterns within a sequence (seqshowwords, seqwordcount), or search for open reading frames (seqshoworfs). You can manipulate your sequence by performing an in-silico digestion with restriction endonucleases (restrict) and proteases (cleave ). In addition, you can create random sequences for test cases (randseq).

Sequence Alignments

Microarray Analysis