LMG: Softwares
Perl script to identify palindromes and inverted repeats in a given multi-FASTA file |
We have written two perl scripts (inp_seq and run_blast) for identification of palindromes and inverted repeats
1) Run 'inp_seq' to split the multi-FASTA file into single sequence files and all the individual files will be stored in the same folder.
2) Copy all the individual sequence file names in a notepad and save it as separate file.
3) When 'run_blast' is executed, it will ask for file containing individual sequence filenames. After giving the full path to that file, it will carry out BLAST run and stores the output of all the input sequences in a single file named output.
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Download from the links below
inp_seq
run_blast
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C program to calculate AT percent of a given multi-FASTA sequence file
1) The two files (extractATper.c and functionsAT.h) should be in the same directory while running the program. To compile and create an executable type the command below
cc extractATper.c -o exe
2) Run the program by this command
./exe
-file1 should have the multi-FASTA sequences
-file2 should have the FASTA tags/names
3) File2 can be created by typing the following command
grep ">" file1 > file2
4) The output file "results", contains the A+T count and A+T+G+C+N count. From this AT percentage can be calculated using Microsoft excel data sheet.
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Download from the links below
extractATper.c
functionsAT.h
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| Last updated on: Friday,14th March, 2008. |
