HOWTOUSEPP1.txt

HOW TO USE PP1.py *UPDATED VERSION*:

UNCHANGED FROM PREVIOUS VERSION:

You must have Python modules Bio and NumPy installed.

You must have BLOSUM62 text file, proseq.fasta, and dna.fasta in the same directory as the program before running.

Only use BLOSUM62 score matrix provided. This is essential as I removed the comments at the top of the NIH-provided BLOSUM62 file.

With current program, you must use a protein sequence named proseq.fasta and DNA sequence of dnaseq.fasta. These names can be changed by editing lines 9 and 12 of the program.

I have provided proseq.fasta and dnaseq.fasta containing the sequences used for Example 1 within the Test Cases section of provided report.

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NEW VERSION:

This version prompts you to check whether the user wants to implement an affine or length-independent gap penalty. Two sets of prompts are provided, with the first referring to alignment within frames and the second referring to alignment between frames.

For each set, the program will prompt the following:

Affine gap penalty [within/between] frames? (MUST SAY y FOR YES):

Any input other than 'y' will prompt the program to use a length-independent gap penalty. If an affine gap penalty is chosen, the following will be output next:

Desired gap extension penalty [within/between] frames:

A numerical answer must be given as this number will be converted into an integer. The absolute value of this value is passed on to the remainder of the program, so negative or positive values will yield the same result.

The final statement per set of inputs is the following. If 'y' is not provided in response to the first message, the program will skip to this. If 'y' is provided, the program will ask this after the previous statement.

Desired gap extension penalty [within/between] frames:

Similar to the previous question, a numerical answer must be given so that it may be converted to the absolute value of an integer.

After these 4-6 values are input (number of prompts given depends on use of affine/length-dependent gap penalty), the program runs as previously described.
	HOW TO USE PP1.py UPDATED VERSION:

	UNCHANGED FROM PREVIOUS VERSION:

	You must have Python modules Bio and NumPy installed.

	You must have BLOSUM62 text file, proseq.fasta, and dna.fasta in the same directory as the program before running.

	Only use BLOSUM62 score matrix provided. This is essential as I removed the comments at the top of the NIH-provided BLOSUM62 file.

	With current program, you must use a protein sequence named proseq.fasta and DNA sequence of dnaseq.fasta. These names can be changed by editing lines 9 and 12 of the program.

	I have provided proseq.fasta and dnaseq.fasta containing the sequences used for Example 1 within the Test Cases section of provided report.

	-------

	NEW VERSION:

	This version prompts you to check whether the user wants to implement an affine or length-independent gap penalty. Two sets of prompts are provided, with the first referring to alignment within frames and the second referring to alignment between frames.

	For each set, the program will prompt the following:

	Affine gap penalty [within/between] frames? (MUST SAY y FOR YES):

	Any input other than 'y' will prompt the program to use a length-independent gap penalty. If an affine gap penalty is chosen, the following will be output next:

	Desired gap extension penalty [within/between] frames:

	A numerical answer must be given as this number will be converted into an integer. The absolute value of this value is passed on to the remainder of the program, so negative or positive values will yield the same result.

	The final statement per set of inputs is the following. If 'y' is not provided in response to the first message, the program will skip to this. If 'y' is provided, the program will ask this after the previous statement.

	Desired gap extension penalty [within/between] frames:

	Similar to the previous question, a numerical answer must be given so that it may be converted to the absolute value of an integer.

	After these 4-6 values are input (number of prompts given depends on use of affine/length-dependent gap penalty), the program runs as previously described.