Package Bio :: Package SeqUtils
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Package SeqUtils

source code

Submodules [hide private]

Classes [hide private]
  ProteinX
  MissingTable
Functions [hide private]
 
reverse(seq)
Reverse the sequence.
source code
 
GC(seq)
calculates G+C content
source code
 
GC123(seq)
calculates total G+C content plus first, second and third position
source code
 
GC_skew(seq, window=100)
calculates GC skew (G-C)/(G+C)
source code
 
xGC_skew(seq, window=1000, zoom=100, r=300, px=100, py=100)
calculates and plots normal and accumulated GC skew (GRAPHICS !!!)
source code
 
molecular_weight(seq) source code
 
nt_search(seq, subseq)
search for a DNA subseq in sequence use ambiguous values (like N = A or T or C or G, R = A or G etc.) searches only on forward strand
source code
 
makeTableX(table) source code
 
seq3(seq)
Method that returns the amino acid sequence as a list of three letter codes.
source code
 
translate(seq, frame=1, genetic_code=1, translator=None)
translation of DNA in one of the six different reading frames
source code
 
GC_Frame(seq, genetic_code=1)
just an alias for six_frame_translations
source code
 
six_frame_translations(seq, genetic_code=1)
nice looking 6 frame translation with GC content - code from xbbtools similar to DNA Striders six-frame translation
source code
 
fasta_uniqids(file)
checks and changes the name/ID's to be unique identifiers by adding numbers
source code
 
quick_FASTA_reader(file)
simple and FASTA reader, preferable to be used on large files
source code
 
apply_on_multi_fasta(file, function, *args)
apply function on each sequence in a multiple FASTA file
source code
 
quicker_apply_on_multi_fasta(file, function, *args)
apply function on each sequence in a multiple FASTA file
source code
Variables [hide private]
  proteinX = ProteinX()
Function Details [hide private]

reverse(seq)

source code 

Reverse the sequence. Works on string sequences.

seq3(seq)

source code 

Method that returns the amino acid sequence as a list of three letter codes. Output follows the IUPAC standard plus 'Ter' for terminator. Any unknown character, including the default unknown character 'X', is changed into 'Xaa'. A noncoded aminoacid selenocystein is recognized (Sel, U).