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.
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
), or search for specific patterns within a sequence (seqwordcount
). 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
).