SeqAnalyzer

[moozeq]

Amino acid sequences analyzer. Performing complex analysis per sequence and on all of them.

Main features:

• use SeqRecord for amino acid sequences
• perform complex analysis
• retrieve results as two dictionaries

Analysis should contain:

• isoelectric point for protein sequences
• standard aa in protein sequences, in a list of dicts (amino_acids)
• aromaticity for protein sequences according to Lobry 1994 method
• amino acid percentage content based aa content in protein sequences
• instability indexes for protein sequences according to Guruprasad et al 1990
• flexibility of protein sequences according to Vihinen, 1994
• fraction of helix, turn and sheet for protein sequence
• GRAVY of protein sequences according to Kyte and Doolittle
• molar extinction coefficients for protein sequences
• median length of sequences
• average length of sequences
• standard deviation od sequence length
• Calculated 'N' and 'C' terminus amino acid occurrences frequencies

Responsible person: @KacDom

[erpeg]

According to calculations. It would be handy for me, if some calculated values, that reach enormous long values after decimal points (e.g. % amino acid content) were rounded (3, maybe 4 decimal points - at this moment it's hard for me to define precisely, I will need to test it).

Furthermore I'd be glad, if we clarified what happens with dictionary-format passed data (i.e. aa composition, N and C terminus aa occurences, etc.) if specific aa/nuclotide/w/e is not present in sequence. I need to have all aa/nucletoides as keys in dictionary even if their value is equal to 0.

Last but not least - are abbreviaitons that can indicate one of two amino acids also present in aa composition dictionaries, i.e.

Abreviation	aa
B	Aspartic acid or Asparagine
Z	Glutamic acid or Glutamine
X	Any amino acid
J	Leucine or Isoleucine
EDIT: I forgot to mention, I need also a dictionary with units of each calculated parameter (e.g. {'molecular_weight': 'Molecular weight [Da], 'theoretical_pi': 'Isoelectric point [pH]'} )
Thanks in advance :)

[moozeq]

Todo tasks:

• more tests and more complex tests