Icarus Class: Seq
Information about a sequence - name, the actual sequence itself, the name of the database it is from, any comments, and other information.
name Attribute may stay unnamed in attribute list. 
  Sequence name.
dbName  
  Databank name.
cmnt  
  Short description of the sequence.
state  
  Sequence state. 's' for original sequence, 'f' for a fragment, 'e' for an edited sequence, or null (zero) if unset.
seq  
  The protein or DNA sequence as a string.
stream  
  Print stream.
app
Appends a string to a sequence, or reads a sequence from a file. Only one of string ('s') or file ('file') should be given. The function filters out all non-sequence characters such as digits, spaces, and line feeds. This will change the sequence object. Call $Seq.make after the last sequence fragment has been appended to finalize your $Seq.app changes.
s Argument may stayunnamed in argument list. 
Additional sequence as a string.
file  
Filename. If provided, reads a sequence from a named file.
crc
Returns the Cyclic Redundancy Check of a sequence, encoded in a 6 character string.
cut
Cuts a part out of a sequence
from Argument may stayunnamed in argument list. 
Start position
to  
End position
Seq
len
Returns the length of a sequence.
make
Must be called to commit a sequence object after (possibly repeated) use of $Seq.app. This will change the sequence object.
Seq
str
Prints a sequence in various formats.
format Argument may stayunnamed in argument list. fasta 
Name of a defined sequence output format Supported formats are: string, embl, genbank, swiss, fasta, plain pir, gcg, proteinchart and prett.,
width 60 
Output width in seqeunce characters per line.
useStream n 
y n
Specifies whether the method should print to a stream already opened.
trim
Trims characters from a sequence
skipchar Argument may stayunnamed in argument list. 
Characters to skip. Defaults to removing gap characters '.' and '-', and stopping at first '*' stop. If characters are specified, this '*' stop functionality is not available. See also the related string trim function for removing whitespace from a string.
trunc
Truncates a sequence by the specified number of characters.
len Argument may stayunnamed in argument list. 
Number of bases or residues to delete.
Seq
type
Returns the type of a sequence