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GC123(seq)
calculates total G+C content plus first, second and third position |
source code
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GC_skew(seq,
window=100)
calculates GC skew (G-C)/(G+C) |
source code
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xGC_skew(seq,
window=1000,
zoom=100,
r=300,
px=100,
py=100)
calculates and plots normal and accumulated GC skew (GRAPHICS !!!) |
source code
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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
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seq3(seq)
Method that returns the amino acid sequence as a list of three letter
codes. |
source code
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translate(seq,
frame=1,
genetic_code=1,
translator=None)
translation of DNA in one of the six different reading frames |
source code
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GC_Frame(seq,
genetic_code=1)
just an alias for six_frame_translations |
source code
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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
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fasta_uniqids(file)
checks and changes the name/ID's to be unique identifiers by adding
numbers |
source code
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quick_FASTA_reader(file)
simple and FASTA reader, preferable to be used on large files |
source code
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apply_on_multi_fasta(file,
function,
*args)
apply function on each sequence in a multiple FASTA file |
source code
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quicker_apply_on_multi_fasta(file,
function,
*args)
apply function on each sequence in a multiple FASTA file |
source code
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