AmproCode-scripts

A database search algorithm proving the theoretical feasiblility of AmproCode and computational simulation to estimate the coverage of the whole proteome and secretome

Usage

Searching from fasta

All scripts are located in "scripts", the first option is the sequence database(fasta), followed by "code" of the sample. For example:

python search_CKMDE.py ../databases/secreted_seq.fasta 0.97 1 0.98 0.49

rank= 1 P0DMC3|ELA_HUMAN 7.468776545216382e-05 1

rank= 2 Q9BYW3|DB126_HUMAN 0.02542741131229176 1

rank= 3 P16860|ANFB_HUMAN 0.029564160560074715 1

rank= 4 P10092|CALCB_HUMAN 0.038327614363006135 1

rank= 5 P11686|PSPC_HUMAN 0.05956680608347864 1

... ...

python search_CKMDEY.py ../databases/secreted_seq.fasta 2.06 0.01 1.0 0.95 1.00

rank= 1 P10997|IAPP_HUMAN 0.000384893975971079 2

rank= 2 Q765I0|UTS2B_HUMAN 0.000384893975971079 2

rank= 3 Q6ZRU5|YQ032_HUMAN 0.011808715519036728 1

rank= 4 P60022|DEFB1_HUMAN 0.01356380669196311 1

rank= 5 P04808|REL1_HUMAN 0.014103506613592942 1

... ...

python search_CKMDE.py ../databases/UP000005640_9606.fasta 6 2 2 11

rank= 1 sp|P59666 0 2

rank= 2 sp|P01308 0 2

rank= 3 sp|Q4KMG9 0.00046825665561844865 1

rank= 4 sp|Q9BY78 0.0006505979351558722 1

rank= 5 sp|Q76LX8 0.000841947322775427 1

... ...

Each line of the ouput: rank, protein_name, cos_distance, degeneracy

Note: cos_similarity = 1 - cos_distance

Simulation for noises

Adding random noise for “code” of each protein in proteome, the first option is the sequence database(fasta), followed by sigma of the noise(draw from gaussian). For example:

python comp2seq_CK.py ../databases/secreted_seq.fasta 0.01

2578 top1= 0.06361520558572537 top3= 0.15438324282389448

Output: number of code, probabilityof the correct answer appearing in the top1 ranking, probabilityof the correct answer appearing in the top3 ranking.