Team:UCSC/Software

Software at UCSC

F.O.C.U.S


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sequenceAnalysis


1.1 What is it for?

The sequenceAnalysis program is a tool for providing efficient, large scale analysis of amino acid sequences. It works very much like the software ProtParam designed by ExPASy. However, unlike ProtParam, this program has the advantage of reading and computing the physical and chemical properties of multiple proteins all at once.

1.2 Program Specifications

This program was written using the most recent version of the Python programming language, Python 3.4.3. It is designed to work as module, which can be imported to any program to access all or specific functions that the user requires. An added benefit of the modular design is that it can be easily edited to provide further functionality. At this point, this program is made up of two classes: ProteinParam and FastAReader.

This class was written by UCSC iGEM team members Cristian Camacho, Jairo Navarro, and Raymond Bryan. It was developed in the course BME 160: Research Programming in the Life Sciences, and serves as the backbone for two other programs that are being submitted: CodonBiasGenerator and FOCUS.

2.1 Attributes

  • aa2mw : A dictionary of the molecular weights of all 20 amino acids
  • mwH20 : A float value corresponding to the molecular weight of water
  • aa2abs280 : Dictionary of the absorbance values of Tyrosine, Tryptophan and Cysteine at a wavelength of 280 nm.
  • aa2chargePos : Dictionary of the positive charge values of Lysine, Arginine and Histidine
  • aa2chargeNeg : Dictionary of the negative charge value of Aspartic Acid, Glutamic Acid, Cysteine and Tyrosine.
  • aaNterm : Float value of the charge
  • aaCterm : Float value of
  • validAA : An empty dictionary which will contain the counts of valid amino acids in a specific protein sequence.

2.2 Methods

  • aaCount( ) : Iterates through the amino acid sequence and returns a single integer count of valid amino acid characters found.
  • aaComposition ( ) : Returns the validAA dictionary with the valid amino acids and their counts for a specific protein.
  • pI ( ) : Estimates the theoretical isoelectric point of a protein by iterating through every pH value until it finds the one that results in a net charge that is closest to zero.
  • charge ( ) : Calculate the net charge at a particular pH, using the pKa of each charged Amino acid and the Nterminus and Cterminus
  • molarExtinction ( ) : Estimates the molar extinction coefficient based on the number and extinction coefficients of tyrosines, tryptophans, and cysteines.
  • massExtinction ( ) : Calculates the mass extinction by dividing the molar extinction value by the molecular weight of the corresponding protein.
  • molecularWeight ( ) : Calculates a proteins molecular weight by summing the weights of the individual Amino acids and excluding the waters that are released with peptide bond formation.
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Codon Bias Generator


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