SHELL SCRIPT PROGRAMMING

Write a shell script run_progs.sh that will

--> run EMBOSS water and EMBOSS needle program in succession on the same input files

--> take as command-line arguments the names of sequences within sequences.fasta that will be input to water and needle

--> have water save its output in a file whose name is constructed from the sequence name plus the extension ".water.out"

have needle save its output in a file whose name is constructed from the sequence name plus the extension ".needle.out"

For each invocation of water or needle by/within the script, the second sequence in the alignment will be the cloning vector. An example of using the script is

./run_progs.sh sequence1 sequence2 sequence3

Hints:

You will need a loop in your script.

You will need to invoke water and needle with all their necessary parameters specified on the command line.

To force water and needle to use their default values for gap opening and extension penalties, specify the -auto option.

DETAIL ON EMBOSS WATER and NEEDLE

These programs will take in any 2 DNA sequences and compute the best alignment.

A normal run of these programs

1) Needle program

nlt895@tux7:~/b200lab7> needle sequence1.fasta sequence2.fasta Needleman-Wunsch global alignment of two sequences Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [sequence1.needle]: q9.1v2

2) Water program

nlt895@tux7:~/b200lab7> water sequence1.fasta sequence2.fasta Smith-Waterman local alignment of sequences Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [sequence1.water]: seq1.example nlt895@tux7:~/b200lab7>