Bio (Bio Sequencer) Module

The Bio Sequencer module reads DNA or protein sequences prepared by the Bio Editor, which is available from Algorithmic Arts as a separate program. The bio seqences are stored as a .bst file by the Bio Editor.  However BankStep includes a default bio sequence file preloaded with several example DNA and protein sequences, so the Bio Editor is not necessary in order to use the Bio Sequencer.

Special Controls

The drop down menu at the top of the module selects the bio sequence to play. You can select one of up to 24 sequences in the Bio Sequence table that has been processed by the Bio Editor. This table is a system file that is automatically loaded when BankStep starts up, or when you load a BankStep file of the same name in the same directory.  You can also load a bio sequence file directly, from the Files menu.

Each entery on the drop down menu shows the slot number (0-23) of the sequence being addressed, the number of proteins or codons in the sequence [in brackets], and the file name of the sequence at the time it was encoded. If there is no sequence data in a particular slot, the item will display "<no data>" and the sequencer will not step.

The red button on the top left of the module, if in, sets the Bio Sequncer to stop at the end of its sequence; leaving the button out (the default), causes the sequencer to endlessly repeat.

The blue button just below, to the left of the Clock input, if in, causes the sequence to step to a new amino acid every 3 clock ticks.  This is the default, and it is the more scientifically correct setting of 3 DNA steps for each amino acid step.  When the button is out, there are 4 DNA steps for each amino acid step, with the 4th tick repeating the 3rd DNA codon base.  While less scientifically accurate, this setting is often more musically useful.

The amino acids of the bio sequence are displayed in the large gray text area, with the current step highlighted; the DNA codon bases are displayed in the readout just to the top right of the text area, as the 3-letter code, and the current codon step is displayed just above that as both the letter code (A, C, T, G), and the number (0-3) associated with it. The numerical values for the DNA codon bases are: G=0, C=1, T=2, and A=3.

Technically, if the original data was encoded from a protein sequence instesd of from a DNA sequence, the backtranslated DNA sequence will not be entirely accurate, although the musical pattern will still hold, somewhat simplified. Read this for a detailed explanation.

The readout for the sequence step address is to the upper left of the gray text area, just above the column of readout LEDs. The LEDs show the start and end of the sequence, plus the 6 available structure flags, that you may optionally insert during the editing process with the Bio Editor.  See the Bio Editor documentation (available online at the Algorithmic Arts web site) for information about setting and using structure flags.

The amino acid number (0-20) readout is at the upper right of the module, with the label "AA#." Values assigned to the amino acids (in water solubility order), are:

I  =   0  =  ILE  Isoleucine (nonpolar)
F  =   1  =  PHE  Phenylalanine (nonpolar)
V  =   2  =  VAL  Valine     (nonpolar)
L  =   3  =  LEU  Leucine    (nonpolar)
W  =   4  =  TRP  Tryptophan (nonpolar)
A  =   5  =  ALA  Alanine    (nonpolar)
G  =   6  =  GLY  Glycine    (nonpolar)
M  =   7  =  MET  Methionine (nonpolar)
C  =   8  =  CYS  Cysteine   (polar)
Y  =   9  =  TYR  Tyrosine   (polar)
P  =  10  =  PRO  Proline    (nonpolar)
T  =  11  =  THR  Threonine  (polar)
S  =  12  =  SER  Serine     (polar)
H  =  13  =  HIS  Histidine  (basic)
N  =  14  =  ASN  Asparagine (polar)
Q  =  15  =  GLN  Glutamine  (polar)
D  =  16  =  ASP  Aspartate (acidic)
E  =  17  =  GLU  Glutamate (acidic)
K  =  18  =  LYS  Lysine     (basic)
R  =  19  =  ARG  Arginine   (basic)
?  =  20  =  ZOT  End Marker or invalid

Just below the AA# readout is the readout for the sorted AA numbers. Amino acid sorting remaps the amino acid numbers so that the most frequently occurring value is given the first table position, the second most frequently occurring value the second position, and so on - so it works musically with a pitch table that is weighted for more harmonic intervals to be at the start of the table.  This harmonic sorting of pitches is easily done using the harmonic sort option in the sequencer fill utilities. Using the sorted amino acid output gives each protein sequence a different amino acid mapping, which is less useful for scientific work but often can be more musical.

Inputs

Clock (Clk - Value, Yellow LED) sets the rate the sequencer steps to the next DNA codon base. Depending on the setting of the blue button to the left of the clock input, a new amino acid is sequenced upon every 3rd (button out) or 4th (button in) clock tick. When the sequence reaches its end, it rolls over to the start again. Or, if the red button above the Clk label has been clicked in, it will stop at the end of the sequence.

Reset: (Rst - Logical, Orange LED): Resets to the start of the sequence and holds it there as long as the input is held On.

Hold: (Hld - Logical, Red LED): Holds at the current step as long as the input is held On.

Antisense: (Anti - Logical, Blue LED): An On value at this input changes the stepping direction. The blue LED will highlight when the direction is reverse, which steps the sequence backward, reversing the codon and giving its antisense. This is similar to reverse playback on other sequencers, except the DNA codon is spelled reciprocally (A and T are switched, as are G and C), which in turn results in a different amino acid being translated.

Value Outputs

Bio X Adr: The sequence address of the current amino acid.  Note that there are 3 or 4 (depending on blue Clk button setting) clock ticks for each amino step in the sequence.

Bio X AA#: The current Amino Acid Number, 0-20.

Bio X AAs: The current Sorted Amino Acid number, 0-20.

Bio X DNA: The current DNA number, 0-3.

Bio X E4: The 4 element ordering of the current AA (maps to 0-3, ?=4):
    0 = IFVLWAGMP: nonpolar
    1 = HKR: basic
    2 = CYTSNQ: polar
    3 = DE: acidic

Bio X E8: The 8 element ordering of the current AA grouped by chemical and substitution similarities (maps 0-7, ?=8):
    0 = ILVMF: large nonpolar (ILV aliphatic)
    1 = C: nonpolar disulfide-forming
    2 = GP: small moderately nonpolar
    3 = AST: small moderately nonpolar
    4 = YW: large aromatic moderately polar
    5 = NQ: small polar
    6 = DE: negatively charged
    7 = HKR: positively charged

Bio X MVo: Molecular volume order, lowest to highest, for the current AA.

Bio X MWo: Molecular weight order, lowest to highest, for the current AA.

Bio X sMV: Relative Mol Volume - normalized (0-127), for the current AA.

Bio X sMW: Relative Mol Weight, normalized (0-127) for the current AA.

Logical Outputs

Bio X S: Start Flag. True for the duration of the AA, at the start of the sequence.

Bio X E: End Flag.  True for the duration of the AA, at the end of the sequence.

Bio X <> () [] {} |! @# $%: Structure Flags.  True from the start flag marker to the end flag marker, as set by the Bio Editor.

Bio X aC: Amino Acid clock tick.

Bio X dC: DNA clock tick.  This will be 3 to 4 times the rate of the AA clock tick, depending on the setting of the blue Clk button.

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